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annotate gfastats.xml @ 0:5f250ffcb1af draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
author bgruening
date Tue, 08 Mar 2022 21:49:13 +0000
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5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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1 <tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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2 <description>the swiss army knife for genome assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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6 <expand macro="requirements" />
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7 <expand macro="biotools"/>
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8 <version_command>gfastats --version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 gfastats
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11 '$input_file'
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12 #if $mode_condition.selector == 'statistics'
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13 #if $mode_condition.statistics_condition.selector == 'assembly'
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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14 $mode_condition.statistics_condition.expected_genomesize
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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15 #end if
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16 #end if
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17 #if $target_condition.target_option == 'true'
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18 $target_condition.target_sequence
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19 #if $target_condition.include_bed
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20 --include-bed $target_condition.include_bed
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21 #end if
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22 #if $target_condition.exclude_bed
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23 --exclude-bed $target_condition.exclude_bed
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24 #end if
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25 #end if
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26 #if $mode_condition.selector == 'manipulation'
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27 #if $mode_condition.swiss_army_knife
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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28 -k $mode_condition.swiss_army_knife
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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29 #end if
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30 #if $mode_condition.sort
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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31 --sort $mode_condition.sort
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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32 #end if
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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33 $mode_condition.homopolymer_compress
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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34 -o dataset.$mode_condition.output_condition.out_format
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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35 #if $mode_condition.output_condition.out_format == 'fasta'
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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36 #if $mode_condition.output_condition.line_length
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37 --line-length $mode_condition.output_condition.line_length
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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38 #end if
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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39 #else if $mode_condition.output_condition.out_format == 'fasta.gz'
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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40 #if $mode_condition.output_condition.line_length
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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41 --line-length $mode_condition.output_condition.line_length
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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42 #end if
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43 #end if
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44 #else
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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45 #if $mode_condition.statistics_condition.selector == 'size'
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46 --out-size $mode_condition.statistics_condition.out_size
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47 #else if $mode_condition.statistics_condition.selector == 'coordinates'
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48 --out-coord $mode_condition.statistics_condition.out_coord
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49 #else if $mode_condition.statistics_condition.selector == 'assembly'
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50 --nstar-report
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51 #else
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52 --seq-report
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53 $mode_condition.statistics_condition.out_sequence
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54 #end if
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55 $mode_condition.tabular > '$stats'
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56 #end if
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57 #if $mode_condition.selector == 'manipulation'
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58 && mv dataset* output_dataset
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59 #end if
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60 ]]></command>
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61 <inputs>
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62 <param name="input_file" argument="--fasta" type="data"
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63 format="fasta,fastq,fastqsanger,gfa1,fasta.gz,fastq.gz,fastqsanger.gz,gfa1.gz"
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64 label="Input file"/>
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65 <conditional name="target_condition">
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66 <param name="target_option" type="select" label="Specify target sequences">
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67 <option value="false">Disabled</option>
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68 <option value="true">Enabled</option>
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69 </param>
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70 <when value="false"/>
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71 <when value="true">
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72 <param name="target_sequence" type="text" value="" label="Target sequence" help="Target specific sequence by header, optionally with coordinates: header[:start-end]">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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73 <sanitizer invalid_char="">
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74 <valid initial="string.digits,string.letters">
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75 <add value=":"/>
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76 <add value="-"/>
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77 <add value="_"/>
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78 <add value="|"/>
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79 <add value=" "/>
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80 </valid>
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81 </sanitizer>
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82 <validator type="regex">[0-9A-Za-z:-_| ]+</validator>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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83 </param>
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84 <param argument="--include-bed" type="data" optional="true"
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85 format="bed" label="Include specific intervals"
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86 help="Generates output on a subset list of headers or coordinates
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87 in 0-based bed format. It can be combined with --exclude-bed. Optional"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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88 <param argument="--exclude-bed" type="data" format="bed" optional="true"
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89 label="Exclude specific intervals"
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90 help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed Optional"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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91 </when>
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92 <when value="false"/>
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93 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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94 <conditional name="mode_condition">
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95 <param name="selector" type="select" label="Tool mode">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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96 <option value="statistics">Summary statistics generation</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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97 <option value="manipulation">Genome assembly manipulation</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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98 </param>
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99 <when value="manipulation">
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100 <param argument="--swiss-army-knife" type="data"
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101 format="text" label="SAK input file" optional="true"
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102 help="Set of instructions provided as an ordered list"/>
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103 <conditional name="output_condition">
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104 <param argument="--out-format" type="select"
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105 label="Output format" help="Outputs selected sequences.">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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106 <option value="fasta">FASTA</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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107 <option value="fasta.gz">FASTA.gz</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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108 <option value="fastq">FASTQ</option>
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109 <option value="fastq.gz" selected="true">FASTQ.gz</option>
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110 <option value="gfa">GFA</option>
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111 <option value="gfa.gz">GFA.gz</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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112 </param>
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113 <when value="fasta">
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114 <expand macro="length_macro"/>
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115 </when>
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116 <when value="fasta.gz">
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117 <expand macro="length_macro"/>
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118 </when>
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119 <when value="fastq"/>
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120 <when value="fastq.gz"/>
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121 <when value="gfa"/>
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122 <when value="gfa.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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123 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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124 <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending used the sequence/path header.">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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125 <option value="" selected="true">Disabled</option>
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126 <option value="ascending">Ascending</option>
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127 <option value="descending">Descending</option>
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128 <option value="largest">Largest</option>
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129 <option value="smallest">Smallest</option>
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130 </param>
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131 <param argument="--homopolymer-compress" type="boolean" truevalue="--homopolymer-compress" falsevalue="" checked="false"
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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132 label="Homopolymer compression" help="Compress all the homopolymers in the input"/>
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133 </when>
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134 <when value="statistics">
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135 <conditional name="statistics_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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136 <param name="selector" type="select" label="Report mode">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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137 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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138 <option value="size">Scaffold, contig or gap sizes (--out-size)</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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139 <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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140 <option value="sequence">Sequence statistics (--seq-report)</option>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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141 </param>
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142 <when value="size">
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143 <param argument="--out-size" type="select" label="Feature for reporting sizes"
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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144 help="Generate a tabular file with the sequence sizes">
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145 <option value="s">Scaffolds</option>
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146 <option value="c">Contigs</option>
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147 <option value="g">Gaps</option>
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148 </param>
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149 </when>
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150 <when value="coordinates">
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151 <param argument="--out-coord" type="select" label="BED coordinares feature"
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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152 help="Generates bed coordinates of given feature. Default: agp">
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153 <option value="a">AGP</option>
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154 <option value="c">Contigs</option>
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155 <option value="g">Gaps</option>
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156 </param>
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157 </when>
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158 <when value="assembly">
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159 <param name="expected_genomesize" type="integer" min="0" optional="true"
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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160 label="Expected genome size" help="Estimated genome size. This parameter is optional, but required for NG* statistics."/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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161 </when>
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162 <when value="sequence">
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163 <param argument="--out-sequence" type="boolean" truevalue="--out-sequence" falsevalue="" checked="false"
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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164 label="Report actual sequence" help="It reports also the actual sequence"/>
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165 </when>
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166 </conditional>
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167 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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168 label="Tabular-format output" help="Generate output in tabular format"/>
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169 </when>
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170 </conditional>
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171 </inputs>
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172 <outputs>
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173 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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174 <filter>mode_condition['selector'] == 'statistics'</filter>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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175 <change_format>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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176 <when input="tabular" value="false" format="text"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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diff changeset
177 </change_format>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
178 </data>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
179 <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
180 <filter>mode_condition['selector'] == 'manipulation'</filter>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
181 <change_format>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
182 <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
183 <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
184 <when input="mode_condition.output_condition.out_format" value="fastq" format="fastq"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
185 <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
186 <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
187 <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
188 </change_format>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
189 </data>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
190 </outputs>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
191 <tests>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
192 <!--Test 01 -->
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
193 <test expect_num_outputs="1">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
194 <param name="input_file" value="dataset_01.fastq.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
195 <conditional name="target_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
196 <param name="target_condition" value="true"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
197 <param name="target_sequence" value="S1_1"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
198 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
199 <conditional name="mode_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
200 <param name="selector" value="manipulation"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
201 <param name="swiss_army_knife" value="swiss_army.sak"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
202 <conditional name="output_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
203 <param name="out_format" value="fasta.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
204 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
205 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
206 <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
207 </test>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
208 <!--Test 02 -->
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
209 <test expect_num_outputs="1">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
210 <param name="input_file" value="dataset_01.fastq.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
211 <conditional name="target_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
212 <param name="target_condition" value="true"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
213 <param name="target_sequence" value="S1_1"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
214 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
215 <conditional name="mode_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
216 <param name="selector" value="statistics"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
217 <conditional name="statistics_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
218 <param name="selector" value="size"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
219 <param name="out_size" value="c"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
220 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
221 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
222 <output name="stats" value="test_02_stats.tabular" ftype="tabular"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
223 </test>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
224 <!--Test 03 -->
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
225 <test expect_num_outputs="1">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
226 <param name="input_file" value="dataset_02.fasta.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
227 <conditional name="mode_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
228 <param name="selector" value="statistics"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
229 <conditional name="statistics_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
230 <param name="selector" value="sequence"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
231 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
232 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
233 <output name="stats" value="test_03_stats.tabular" ftype="tabular"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
234 </test>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
235 <!--Test 04 -->
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
236 <test expect_num_outputs="1">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
237 <param name="input_file" value="dataset_03.fasta"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
238 <conditional name="mode_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
239 <param name="selector" value="statistics"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
240 <conditional name="statistics_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
241 <param name="selector" value="assembly"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
242 <param name="expected_genomesize" value="600000"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
243 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
244 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
245 <output name="stats" value="test_04_stats.tabular" ftype="tabular"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
246 </test>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
247 <!--Test 05 -->
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
248 <test expect_num_outputs="1">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
249 <param name="input_file" value="dataset_04.gfa"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
250 <conditional name="mode_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
251 <param name="selector" value="statistics"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
252 <conditional name="statistics_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
253 <param name="selector" value="coordinates"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
254 <param name="out_coord" value="a"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
255 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
256 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
257 <output name="stats" value="test_05_stats.tabular" ftype="tabular"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
258 </test>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
259 <!--Test 06 -->
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
260 <test expect_num_outputs="1">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
261 <param name="input_file" value="dataset_04.gfa"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
262 <conditional name="mode_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
263 <param name="selector" value="manipulation"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
264 <conditional name="output_condition">
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
265 <param name="out_format" value="fasta.gz"/>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
diff changeset
266 </conditional>
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
bgruening
parents:
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267 </conditional>
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268 <output name="output" value="test_06.fasta.gz" ftype="fasta.gz"/>
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269 </test>
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270 <!--Test 07 -->
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271 <test expect_num_outputs="1">
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272 <param name="input_file" value="dataset_03.fasta"/>
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273 <conditional name="mode_condition">
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274 <param name="selector" value="statistics"/>
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275 <conditional name="statistics_condition">
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276 <param name="selector" value="assembly"/>
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277 </conditional>
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278 <param name="tabular" value="false"/>
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279 </conditional>
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280 <output name="stats" value="test_07_stats.tabular" ftype="tabular"/>
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281 </test>
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282 <!--Test 08 -->
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283 <test expect_num_outputs="1">
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284 <param name="input_file" value="dataset_01.fastq.gz"/>
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285 <conditional name="mode_condition">
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286 <param name="selector" value="manipulation"/>
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287 <conditional name="output_condition">
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288 <param name="out_format" value="fasta.gz"/>
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289 </conditional>
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290 <param name="sort" value="ascending"/>
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291 <param name="homopolymer_compress" value="true"/>
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292 </conditional>
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293 <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/>
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294 </test>
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295 </tests>
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296 <help><![CDATA[
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297
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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298 .. class:: infomark
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299
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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300 **Purpose**
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301
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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302 gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless format conversion.
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303
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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304
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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305 .. class:: infomark
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306
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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307 **Metrics details**
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308
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309 Typical fast* metrics include:
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310
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311 - Scaffold, contig and gap size
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312 - Number of scaffolds, contigs and gaps
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313 - Total length of scaffolds, contigs and gaps
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314 - Scaffold, contig, gap N50 and statistics (full N*/NG* statistics with the --nstar-report flag)
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315 - Area under the curve (AuN/AuNG) values for scaffolds, contigs and gaps
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316 - Average scaffold, contig, gap size
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317 - Largest scaffold, contig and gap
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318 - Base composition and GC content
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319 - Soft-masked base counts (lower case bases)
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320
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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321
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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322 Typical gfa metrics include:
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323
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324 - Number of nodes and edges
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325 - Average degree
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326 - Number of connected components, and length of the largets connected component
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327 - Number of dead ends
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328 - Number of disconnected components, and their total length
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329
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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330
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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331 .. class:: infomark
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332
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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333 **Assembly manipulation**
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334
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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335 gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions.
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336
5f250ffcb1af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 6ca9363cc4e0da886aab9accd79d52663247af29"
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337 ]]></help>
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338 <expand macro="citations" />
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339 </tool>