Mercurial > repos > iuc > medaka_consensus

annotate consensus.xml @ 11:4e65663b2567 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author iuc
date Thu, 22 Apr 2021 20:21:17 +0000
parents 5acc1bfac3ab
children 95a9a77b9e47
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11
4e65663b2567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
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1 <tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
1
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2 <description>Assembly polishing via neural networks</description>
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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[
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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 consensus
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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' ## output
1
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47
4
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48 2>&1 | tee '$out_log'
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49 ]]></command>
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50 <inputs>
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51 <param argument="bam" type="data" format="bam" label="Select input alignment"/>
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52 <expand macro="model" argument="--model"/>
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53 <expand macro="b" argument="--batch_size"/>
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54 <conditional name="regions_cond">
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55 <param name="regions_sel" type="select" label="Specify regions to analyse via">
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56 <option value="none">None</option>
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57 <option value="custom">Custom input</option>
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58 <option value="bed">BED file</option>
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59 </param>
2
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60 <when value="none"/>
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61 <when value="custom">
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62 <param argument="custom" type="text" value="" label="Set genomic regions to analyse"/>
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63 </when>
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64 <when value="bed">
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65 <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/>
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66 </when>
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67 </conditional>
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68 <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
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69 <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
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70 <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/>
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71 <param argument="--save_features" type="boolean" truevalue="--save_features" falsevalue="" label="Save features with consensus?"/>
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72 <param argument="--RG" type="text" value="" optional="true" label="Set read group"/>
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73 <param argument="--tag_name" type="text" value="" optional="true" label="Set tag name" help="Two letters."/>
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74 <param argument="--tag_value" type="integer" value="" optional="true" label="Set tag value"/>
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75 <param argument="--tag_keep_missing" type="boolean" truevalue="--tag_keep_missing" falsevalue="" label="Keep alignments when tag is missing?"/>
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76 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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77 <option value="result" selected="true">Result</option>
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78 <option value="log">Log</option>
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79 </param>
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80 </inputs>
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81 <outputs>
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82 <!-- standard -->
2
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83 <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result">
1
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84 <filter>'result' in out</filter>
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85 </data>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
86 <!-- optional -->
2
eeb7fe9d1583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 1
diff changeset
87 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
1
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
88 <filter>'log' in out</filter>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
89 </data>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
90 </outputs>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
91 <tests>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
92 <!-- #1 default -->
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
93 <test expect_num_outputs="1">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
94 <param name="bam" value="alignment.bam"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
95 <output name="out_result">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
96 <assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
97 <has_size value="32624"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
98 </assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
99 </output>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
100 </test>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
101 <!-- #2 -->
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
102 <test expect_num_outputs="2">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
103 <param name="bam" value="alignment.bam"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
104 <param name="model" value="r941_min_fast_g303"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
105 <param name="batch_size" value="99"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
106 <param name="chunk_len" value="9999"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
107 <param name="chunk_ovlp" value="999"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
108 <param name="check_output" value="true"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
109 <param name="save_features" value="true"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
110 <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
parents:
diff changeset
111 <param name="out" value="result,log"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
112 <output name="out_result">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
113 <assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
114 <has_size value="38400"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
115 </assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
116 </output>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
117 <output name="out_log">
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
118 <assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
119 <has_text_matching expression=".+Validating and finalising output data."/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
120 </assert_contents>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
121 </output>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
122 </test>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
123 </tests>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
124 <help><![CDATA[
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
125 .. class:: infomark
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
126
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
127 **What it does**
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
128
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
129 @WID@
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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130
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
131 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"
iuc
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132
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
133 **Input**
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
134
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
135 Alignment (BAM)
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
136
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
137 **Output**
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
138
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
139 Results (H5/HDF)
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
140
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
141 **References**
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
142
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
143 @REFERENCES@
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
144 ]]></help>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
145 <expand macro="citations"/>
ddf77d35a607 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
146 </tool>