Mercurial > repos > iuc > medaka_consensus

annotate consensus.xml @ 19:6cd17fecb4ef draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:57:32 +0000
parents 1e1270416a97
children
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rev   line source
19
6cd17fecb4ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
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1 <tool id="medaka_consensus" name="medaka inference tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description> inference from a trained model and alignments.</description>
1
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
2
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9 ## initialize
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10 ln -s '${bam}' alignment.bam &&
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11 ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&
1
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12
11
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13 ## Possibly new options bam_chunk and bam_workers. Should we be setting these?
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14
2
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15 ## run
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16 medaka inference
2
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17 ## optional
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18 --debug ## increase log level
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19 --threads \${GALAXY_SLOTS:-4}
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20 --batch_size $batch_size
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21 #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
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22 --regions
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23 #if $regions_cond.regions_sel == 'custom'
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24 '$regions_cond.custom'
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25 #else if $regions_cond.regions_sel == 'bed'
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26 '$regions_cond.bed'
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27 #end if
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28 #end if
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29 --chunk_len $chunk_len
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30 --chunk_ovlp $chunk_ovlp
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31 --model $model
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32 $check_output
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33 $save_features
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34 #if $RG
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35 --RG '$RG'
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36 #end if
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37 #if $tag_name
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38 --tag_name '$tag_name'
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39 #end if
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40 #if str($tag_value):
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41 --tag_value $tag_value
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42 #end if
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43 $tag_keep_missing
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44 ## required
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45 alignment.bam ## bam
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46 '$out_result' 2>&1 | tee log.txt
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47 ]]></command>
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48 <inputs>
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49 <param argument="bam" type="data" format="bam" label="Select input alignment"/>
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50 <expand macro="model" argument="--model"/>
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51 <expand macro="b" argument="--batch_size"/>
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52 <conditional name="regions_cond">
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53 <param name="regions_sel" type="select" label="Specify regions to analyse via">
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54 <option value="none">None</option>
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55 <option value="custom">Custom input</option>
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56 <option value="bed">BED file</option>
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57 </param>
2
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58 <when value="none"/>
1
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59 <when value="custom">
2
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60 <param argument="custom" type="text" value="" label="Set genomic regions to analyse"/>
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61 </when>
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62 <when value="bed">
2
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63 <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/>
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64 </when>
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65 </conditional>
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66 <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
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67 <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
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68 <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/>
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69 <param argument="--save_features" type="boolean" truevalue="--save_features" falsevalue="" label="Save features with consensus?"/>
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70 <param argument="--RG" type="text" value="" optional="true" label="Set read group"/>
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71 <param argument="--tag_name" type="text" value="" optional="true" label="Set tag name" help="Two letters."/>
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72 <param argument="--tag_value" type="integer" value="" optional="true" label="Set tag value"/>
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73 <param argument="--tag_keep_missing" type="boolean" truevalue="--tag_keep_missing" falsevalue="" label="Keep alignments when tag is missing?"/>
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74 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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75 <option value="result" selected="true">Result</option>
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76 <option value="log">Log</option>
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77 </param>
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78 </inputs>
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79 <outputs>
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80 <!-- standard -->
2
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81 <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result">
1
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82 <filter>'result' in out</filter>
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83 </data>
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84 <!-- optional -->
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85 <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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86 <filter>'log' in out</filter>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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87 </data>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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88 </outputs>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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89 <tests>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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90 <!-- #1 default -->
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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91 <test expect_num_outputs="1">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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92 <param name="bam" value="alignment.bam"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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93 <output name="out_result">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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94 <assert_contents>
19
6cd17fecb4ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 17
diff changeset
95 <has_size value="26144"/>
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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96 </assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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97 </output>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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98 </test>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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99 <!-- #2 -->
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
100 <test expect_num_outputs="2">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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101 <param name="bam" value="alignment.bam"/>
19
6cd17fecb4ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 17
diff changeset
102 <param name="model" value="r941_min_fast_g507"/>
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
103 <param name="batch_size" value="99"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
104 <param name="chunk_len" value="9999"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
105 <param name="chunk_ovlp" value="999"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
106 <param name="check_output" value="true"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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107 <param name="save_features" value="true"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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108 <param name="tag_keep_missing" value="true"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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109 <param name="out" value="result,log"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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110 <output name="out_result">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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111 <assert_contents>
19
6cd17fecb4ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 17
diff changeset
112 <has_size value="27104"/>
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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113 </assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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114 </output>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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115 <output name="out_log">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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116 <assert_contents>
19
6cd17fecb4ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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diff changeset
117 <has_text_matching expression=".+Running prediction at full precision"/>
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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118 </assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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119 </output>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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120 </test>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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121 </tests>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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122 <help><![CDATA[
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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123 .. class:: infomark
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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124
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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125 **What it does**
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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126
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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127 @WID@
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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128
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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129 The module *consensus* runs inference from a trained model and alignments.
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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130
15
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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parents: 11
diff changeset
131 ----
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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132
15
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
133 .. class:: infomark
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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parents: 11
diff changeset
134
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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diff changeset
135 **Inputs and outputs**
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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136
15
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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diff changeset
137 Medaka requires a BAM file as input, and generates a Hierarchical Data Format (H5/HDF) datafile.
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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parents: 11
diff changeset
138
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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139
15
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
140 @MODELS@
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
141
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
142 ----
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
143
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
144 .. class:: infomark
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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145
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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146 **References**
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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147
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
148 @REFERENCES@
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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149 ]]></help>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
150 <expand macro="citations"/>
19
6cd17fecb4ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
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diff changeset
151 </tool>