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annotate kma_map.xml @ 2:3cd89604dffd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma commit f040316174672d9e3ce53b1873ab07cff1128940
author iuc
date Mon, 15 Dec 2025 21:59:27 +0000
parents 4b3fca68379b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
3cd89604dffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma commit f040316174672d9e3ce53b1873ab07cff1128940
iuc
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1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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2 <description></description>
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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3 <macros>
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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4 <import>macros.xml</import>
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5 </macros>
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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6 <requirements>
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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7 <requirement type="package" version="@TOOL_VERSION@">kma</requirement>
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8 </requirements>
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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9 <version_command>kma -v</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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12 kma
2
3cd89604dffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma commit f040316174672d9e3ce53b1873ab07cff1128940
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13 -t "\${GALAXY_SLOTS:-1}"
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14 -t_db '${kma_index.fields.path}'
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3cd89604dffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma commit f040316174672d9e3ce53b1873ab07cff1128940
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15 #if $single_paired.single_paired_selector == "paired_collection":
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16 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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17 #else:
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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18 -i '${single_paired.input_sequences}'
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19 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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20 #if str($settings.advanced) == "advanced"
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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21 #if str($settings.kmer_size)
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22 -k '${settings.kmer_size}'
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23 #end if
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24 #if str($settings.p_value)
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25 -p '${settings.p_value}'
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26 #end if
1
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27 $settings.exhaustive_mode
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28 ${settings.decontaminate}
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29 ${settings.dense}
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30 ${settings.ref_fsa}
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31 ${settings.matrix}
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32 ${settings.all_best_mappings}
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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33 #if str($settings.minimum_phred_score)
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34 -mp '${settings.minimum_phred_score}'
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35 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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36 #if str($settings.cut_5_prime)
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37 -5p '${settings.cut_5_prime}'
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38 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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39 ${settings.only_count_kmers}
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40 #if str($settings.min_id)
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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41 -ID '${settings.min_id}'
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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42 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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43 #if str($settings.base_call_depth)
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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44 -bcd '${settings.base_call_depth}'
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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45 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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46 #if str($settings.minimum_mapping_quality)
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47 -mq '${settings.minimum_mapping_quality}'
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48 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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49 #if str($settings.reward)
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50 -reward '${settings.reward}'
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51 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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52 #if str($settings.penalty)
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53 -penalty '${settings.penalty}'
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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54 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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55 #if str($settings.gapopen)
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56 -gapopen '${settings.gapopen}'
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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57 #end if
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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58 #if str($settings.gapextend)
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59 -gapextend '${settings.gapextend}'
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60 #end if
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61 ${settings.force_end_to_end}
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62 -per $settings.pairing_reward
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63 ${settings.set_cge_penalties_and_rewards}
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64 #end if
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65 -o output
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66
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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67 #if str($settings.advanced) == "advanced" and $settings.matrix
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68 && gunzip output.mat.gz
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69 #end if
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70 && gunzip output.frag.gz
e74a31040224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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71 ]]>
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72 </command>
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73 <inputs>
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74 <conditional name="single_paired">
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75 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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76 <option value="paired_collection">Paired collection</option>
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77 <option selected="True" value="single">Single-end data</option>
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78 </param>
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79 <when value="paired_collection">
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80 <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Paired reads" help="FASTQ datasets" />
0
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81 </when>
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82 <when value="single">
1
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83 <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
0
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84 </when>
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85 </conditional>
1
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86 <param argument="-t_db" name="kma_index" type="select">
0
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87 <options from_data_table="kma_index">
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88 <validator type="no_options" message="No KMA index available" />
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89 </options>
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90 </param>
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91 <conditional name="settings">
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92 <param name="advanced" type="select" label="Specify advanced parameters">
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93 <option value="simple" selected="true">No, use program defaults</option>
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94 <option value="advanced">Yes, see full parameter list.</option>
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95 </param>
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96 <when value="simple">
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97 </when>
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98 <when value="advanced">
1
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99 <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
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100 <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
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101 <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
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102 <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
2
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103 <param argument="-dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
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104 <param argument="-ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
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105 <param argument="-matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />
1
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106 <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
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107 <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
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108 <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
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109 <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
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110 <param argument="-ID" name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
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111 <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
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112 <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />
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113 <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />
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114 <param argument="-reward" type="integer" min="1" value="1" max="100" label="Score for match" />
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115 <param argument="-penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />
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116 <param argument="-gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />
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117 <param argument="-gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />
1
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118 <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />
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119 <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />
0
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120 </when>
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121 </conditional>
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122 </inputs>
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123 <outputs>
2
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124 <data name="result_overview" label="${tool.name} on ${on_string}: Result overview" format="tabular" from_work_dir="output.res" />
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125 <data name="consensus_alignment" label="${tool.name} on ${on_string}: Consensus alignment" format="txt" from_work_dir="output.aln" />
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126 <data name="consensus_sequences" label="${tool.name} on ${on_string}: Consensus sequences" format="fasta" from_work_dir="output.fsa" />
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127 <data name="read_mapping" label="${tool.name} on ${on_string}: Read mapping info" format="tabular" from_work_dir="output.frag" />
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128 <data name="assembly_matrix" label="${tool.name} on ${on_string}: Assembly matrix" format="tabular" from_work_dir="output.mat">
0
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129 <filter>settings['matrix']</filter>
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130 </data>
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131 </outputs>
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132 <tests>
2
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133 <test expect_num_outputs="4">
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134 <conditional name="single_paired">
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135 <param name="single_paired_selector" value="single"/>
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136 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
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137 </conditional>
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138 <conditional name="settings">
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139 <param name="advanced" value="advanced"/>
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140 <param name="kmer_size" value="8"/>
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141 </conditional>
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142 <param name="kma_index" value="test_index"/>
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143 <output name="result_overview" ftype="tabular">
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144 <assert_contents>
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145 <has_n_lines n="3"/>
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146 <has_n_columns n="11"/>
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147 <has_text text="#Template"/>
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148 <has_text text="b0842_1"/>
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149 </assert_contents>
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150 </output>
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151 <output name="consensus_alignment" ftype="txt">
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152 <assert_contents>
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153 <has_n_lines n="170"/>
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154 <has_text text="b0842_1"/>
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155 <has_text text="query" n="42"/>
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156 <has_text text="template" n="42"/>
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157 </assert_contents>
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158 </output>
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159 <output name="consensus_sequences" ftype="fasta">
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160 <assert_contents>
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161 <has_line_matching expression="^>.*" n="2"/>
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162 <has_line_matching expression="^>b0842_1"/>
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163 </assert_contents>
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164 </output>
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165 <output name="read_mapping" ftype="tabular">
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166 <assert_contents>
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167 <has_n_lines n="513"/>
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168 <has_n_columns n="7"/>
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169 <has_text text="b0842_1"/>
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170 </assert_contents>
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171 </output>
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172 </test>
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173 <test expect_num_outputs="5">
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174 <conditional name="single_paired">
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175 <param name="single_paired_selector" value="single"/>
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176 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
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177 </conditional>
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178 <conditional name="settings">
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179 <param name="advanced" value="advanced"/>
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180 <param name="kmer_size" value="8"/>
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181 <param name="matrix" value="true"/>
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182 </conditional>
0
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183 <param name="kma_index" value="test_index"/>
2
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184 <output name="assembly_matrix" ftype="tabular">
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185 <assert_contents>
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186 <has_n_lines n="2578"/>
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187 <has_n_columns n="7" comment="#"/>
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188 <has_line_matching expression="^A&#009;.*"/>
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189 <has_line_matching expression="^T&#009;.*"/>
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190 <has_line_matching expression="^C&#009;.*"/>
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191 <has_line_matching expression="^G&#009;.*"/>
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192 </assert_contents>
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193 </output>
0
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194 </test>
2
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195 <test expect_num_outputs="4">
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196 <conditional name="single_paired">
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197 <param name="single_paired_selector" value="paired_collection"/>
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198 <param name="input_pair">
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199 <collection type="paired">
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200 <element name="forward" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/>
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201 <element name="reverse" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/>
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202 </collection>
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203 </param>
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204 </conditional>
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205 <conditional name="settings">
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206 <param name="advanced" value="advanced"/>
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207 <param name="kmer_size" value="8"/>
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208 </conditional>
0
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209 <param name="kma_index" value="test_index"/>
2
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210 <output name="result_overview" ftype="tabular">
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211 <assert_contents>
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212 <has_n_lines n="4"/>
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213 <has_n_columns n="11"/>
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214 <has_text text="#Template"/>
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215 <has_text text="b0842_1"/>
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216 </assert_contents>
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217 </output>
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218 <output name="consensus_alignment" ftype="txt">
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219 <assert_contents>
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220 <has_n_lines n="255"/>
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221 <has_text text="b0842_1"/>
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222 <has_text text="query" n="63"/>
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223 <has_text text="template" n="63"/>
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224 </assert_contents>
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225 </output>
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226 <output name="consensus_sequences" ftype="fasta">
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227 <assert_contents>
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228 <has_line_matching expression="^>.*" n="3"/>
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229 <has_line_matching expression="^>b0842_1"/>
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230 </assert_contents>
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231 </output>
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232 <output name="read_mapping" ftype="tabular">
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233 <assert_contents>
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234 <has_n_lines n="1048"/>
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235 <has_n_columns n="7"/>
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236 <has_text text="b0842_1"/>
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237 </assert_contents>
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238 </output>
0
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239 </test>
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240 </tests>
2
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241 <help><![CDATA[
0
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242
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243 When the mapping is done KMA will produce the following files:
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244
2
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245 * .res A result overview giving the most common statistics for each mapped template.
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246 * .fsa The consensus sequences drawn from the alignments.
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247 * .aln The consensus alignment of the reads against their template.
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248 * .frag Mapping information on each mapped read, columns are:
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249 1. read
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250 2. number of equally well mapping templates
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251 3. mapping score
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252 4. start position
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253 5. end position (w.r.t. template)
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254 6. the choosen template.
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255
2
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256 * .mat Base counts on each position in each template, (only if `-matrix` is enabled)
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257 ]]></help>
0
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258 <expand macro="citations" />
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259 </tool>