Mercurial > repos > iuc > medaka_variant

annotate variant.xml @ 3:009673c8ac31 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
author iuc
date Tue, 01 Sep 2020 07:05:40 +0000
parents 740e5a738658
children 43bc582c0556
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rev   line source
0
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1 <?xml version="1.0"?>
3
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2 <tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
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3 <description>Probability decoding</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
1
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10 ## initialize
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11 @REF_FASTA@
0
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12
1
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13 ## run
740e5a738658 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
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14 medaka variant
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15 ## optional
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16 --debug
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17 #if $region
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18 --region '${region}'
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19 #end if
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20 $verbose
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21 ## required
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22 reference.fa
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23 #for $current in $inputs
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24 '$current'
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25 #end for
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26 '$out_result' ## output
0
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27
3
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28 2>&1 | tee '$out_log'
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29
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30 #if $out_annotated
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31 && python '$__tool_directory__/annotateVCF.py' '$out_result' '$in_mpileup' '$out_annotated'
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32 #end if
1
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33 ]]></command>
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34 <inputs>
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35 <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
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36 <expand macro="reference"/>
3
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37 <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','.">
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38 <sanitizer invalid_char="">
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39 <valid initial="string.ascii_letters,string.digits">
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40 <add value="_"/>
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41 <add value=","/>
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42 <add value="."/>
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43 </valid>
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44 </sanitizer>
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45 </param>
0
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46 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
3
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47
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48 <conditional name="output_annotated">
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49 <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires pileup file)">
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50 <option value="true" selected="true">Output annotated VCF</option>
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51 <option value="false">Don't output annotated VCF</option>
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52 </param>
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53 <when value="true">
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54 <param name="in_mpileup" type = "data" format="pileup" optional="false" label="Mpileup to annotate the VCF"/>
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55 </when>
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56 </conditional>
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57 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
0
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58 </inputs>
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59 <outputs>
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60 <!-- standard -->
3
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61 <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/>
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62 <!-- optional -->
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63 <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated">
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64 <filter>output_annotated_select</filter>
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65 </data>
1
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66 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
3
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67 <filter>output_log_bool</filter>
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68 </data>
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69 </outputs>
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70 <tests>
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71 <!-- #1 default -->
3
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72 <test expect_num_outputs="3">
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73 <param name="inputs" value="medaka_test.hdf"/>
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74 <conditional name="reference_source">
3
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75 <param name="reference_source_selector" value="history"/>
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76 <param name="ref_file" value="ref.fasta"/>
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77 </conditional>
3
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78 <conditional name="output_annotated">
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79 <param name="output_annotated_select" value="true"/>
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80 <param name="in_mpileup" value="annotate_vcf_test.pileup"/>
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81 </conditional>
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82 <param name="output_log_bool" value="true"/>
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83
0
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84 <output name="out_result">
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85 <assert_contents>
3
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86 <has_n_lines n="9"/>
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87 <has_line line="##fileformat=VCFv4.1" />
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
88 <has_line line="##medaka_version=1.0.3" />
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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89 </assert_contents>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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90 </output>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
91 <output name="out_annotated">
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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92 <assert_contents>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
93 <has_n_lines n="16"/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
94 <has_line line="##fileformat=VCFv4.1" />
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
95 <has_line line="##medaka_version=1.0.3" />
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
96 <has_line line="##annotateVCFVersion=0.1" />
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
97 </assert_contents>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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98 </output>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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99 <output name="out_log">
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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100 <assert_contents>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
101 <has_n_lines n="8" />
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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102 </assert_contents>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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103 </output>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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104 </test>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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105 </tests>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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106 <help><![CDATA[
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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107 .. class:: infomark
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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108
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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109 **What it does**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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110
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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111 @WID@
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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112
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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113 The module *variant* decodes probabilities.
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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114
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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115 **Input**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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116
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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117 - reference sequence (FASTA)
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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118 - (several) consensus files (H5/HDF)
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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119
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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120 **Output**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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121
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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122 - decoded probabilities (VCF)
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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123
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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124 **References**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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125
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
126 @REFERENCES@
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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127 ]]></help>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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128 <expand macro="citations"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
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129 </tool>