Mercurial > repos > iuc > medaka_variant

annotate variant.xml @ 17:16fc9856b20a 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 09:58:30 +0000
parents ec699520444c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
16fc9856b20a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
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1 <tool id="medaka_variant" name="medaka vcf tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>decodes variant calls from medaka consensus output</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
10
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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 @REF_FASTA@
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11
4
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12
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13 #if $pool.pool_mode == "Yes":
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14 ## run
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16fc9856b20a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
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15 medaka vcf
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16 ## optional
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17 --debug
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18 #if $regions
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19 --regions '${regions}'
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20 #end if
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21 $verbose
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22 ${ambig_ref}
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23 ${gvcf}
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24 ## required
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25 #for $current in $pool.inputs
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26 '$current'
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27 #end for
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28 reference.fa
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29 #elif $pool.pool_mode == "No":
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30 ## run
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16fc9856b20a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
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31 medaka vcf
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32 ## optional
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33 --debug
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34 #if $regions
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35 --regions '${regions}'
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36 #end if
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37 $verbose
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38 ${ambig_ref}
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39 ${gvcf}
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40 ## required
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41 '$pool.input'
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42 reference.fa
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43 #end if
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44 #if str($output_annotated.output_annotated_select) == 'false':
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45 '$out_variants' 2>&1 | tee log.txt
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46 #else
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47 raw.vcf 2>&1 | tee log.txt
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48 && ln -s '$output_annotated.in_bam' in.bam
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49 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
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50 && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
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51 && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_variants'
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52 #end if
1
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53 ]]></command>
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54 <inputs>
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55 <conditional name="pool">
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56 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?">
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57 <option value="No" selected="true">No</option>
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58 <option value="Yes">Yes</option>
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59 </param>
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60 <when value="Yes">
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61 <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
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62 </when>
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63 <when value="No">
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64 <param name="input" type="data" format="h5" label="Select consensus file(s)"/>
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65 </when>
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66 </conditional>
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67 <expand macro="reference"/>
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68 <param argument="--regions" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','.">
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69 <sanitizer invalid_char="">
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70 <valid initial="string.ascii_letters,string.digits">
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71 <add value="_"/>
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72 <add value=","/>
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73 <add value="."/>
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74 </valid>
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75 </sanitizer>
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76 </param>
0
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77 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
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78 <param argument="--ambig_ref" type="boolean" truevalue="--ambig_ref" falsevalue="" label="Decode variants at ambiguous reference positions?" checked="false"/>
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79 <param argument="--gvcf" type="boolean" truevalue="--gvcf" falsevalue="" label="Output VCF records for reference loci predicted to be non-variant?" checked="false"/>
3
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80 <conditional name="output_annotated">
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81 <param name="output_annotated_select" type="select"
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82 label="Type of VCF to generate"
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83 help="Variant INFO fields in the VCF can be extended to include allele frequency, depth of coverage, etc., but this requires a BAM dataset to calculate those values from.">
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84 <option value="true" selected="true">Write annotated VCF with extended INFO</option>
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85 <option value="false">Write original decoded VCF with minimal INFO field</option>
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86 </param>
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87 <when value="true">
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
88 <param name="in_bam" type="data" format="bam" optional="false" label="BAM to caclulate additional INFO fields from"/>
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
89 <param name="pad" type="integer" min="1" value="25"
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
90 label="Padding width on either side of variant for realignment"
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
91 help="To calculate the additional INFO fields the tool will run medaka tools anntotate, which performs local realignment of the region +- this width around each variant. All calculated new fields will depend on the width chosen, so only change this value if you know what you are doing." />
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
92 </when>
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
93 <when value="false"/>
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
94 </conditional>
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
95 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
96 </inputs>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
97 <outputs>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
98 <data name="out_variants" format="vcf" label="${tool.name} on ${on_string}: called variants"/>
17
16fc9856b20a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 15
diff changeset
99 <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
100 <filter>output_log_bool</filter>
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
101 </data>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
102 </outputs>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
103 <tests>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
104 <!-- #1 default -->
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
105 <test expect_num_outputs="2">
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
106 <conditional name="pool">
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
107 <param name="pool_mode" value="Yes"/>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
108 <param name="inputs" value="medaka_test.hdf,medaka_test.hdf"/>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
109 </conditional>
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
110 <conditional name="reference_source">
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
111 <param name="reference_source_selector" value="history"/>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
112 <param name="ref_file" value="ref.fasta"/>
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
113 </conditional>
10
9fb055604648 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
114 <param name="ambig_ref" value="true"/>
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
115 <conditional name="output_annotated">
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
116 <param name="output_annotated_select" value="true"/>
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
117 <param name="in_bam" value="medaka_test.bam"/>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
118 </conditional>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
119 <param name="output_log_bool" value="true"/>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
120 <output name="out_variants">
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
121 <assert_contents>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
122 <has_n_lines n="18"/>
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
123 <has_line line="##fileformat=VCFv4.1" />
6
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
124 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
125 <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
126 </assert_contents>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
127 </output>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
128 <output name="out_log">
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
129 <assert_contents>
15
ec699520444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 13
diff changeset
130 <has_n_lines n="12" />
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
131 </assert_contents>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
132 </output>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
133 </test>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
134 <!--No pooling-->
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
135 <test expect_num_outputs="2">
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
136 <conditional name="pool">
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
137 <param name="pool_mode" value="No"/>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
138 <param name="input" value="medaka_test.hdf"/>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
139 </conditional>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
140 <conditional name="reference_source">
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
141 <param name="reference_source_selector" value="history"/>
9
43815fa60f3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
parents: 8
diff changeset
142 <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/>
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
143 </conditional>
10
9fb055604648 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
144 <param name="ambig_ref" value="true"/>
4
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
145 <conditional name="output_annotated">
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
146 <param name="output_annotated_select" value="true"/>
2308bc523659 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
147 <param name="in_bam" value="medaka_test.bam"/>
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
148 </conditional>
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
149 <param name="output_log_bool" value="true"/>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
150 <output name="out_variants">
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
151 <assert_contents>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
152 <has_n_lines n="18"/>
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
153 <has_line line="##fileformat=VCFv4.1" />
6
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
154 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
7
28c13c42de01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
iuc
parents: 6
diff changeset
155 <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
156 </assert_contents>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
157 </output>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
158 <output name="out_log">
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
159 <assert_contents>
15
ec699520444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 13
diff changeset
160 <has_n_lines n="9" />
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
161 </assert_contents>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
162 </output>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
163 </test>
6
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
164 <!--No annotation or log-->
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
165 <test expect_num_outputs="1">
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
166 <conditional name="pool">
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
167 <param name="pool_mode" value="No"/>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
168 <param name="input" value="medaka_test.hdf"/>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
169 </conditional>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
170 <conditional name="reference_source">
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
171 <param name="reference_source_selector" value="history"/>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
172 <param name="ref_file" value="ref.fasta"/>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
173 </conditional>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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174 <conditional name="output_annotated">
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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175 <param name="output_annotated_select" value="false"/>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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176 </conditional>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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diff changeset
177 <param name="output_log_bool" value="false"/>
12
0f5f4a208660 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
178 <output name="out_variants">
6
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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179 <assert_contents>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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180 <has_n_lines n="9"/>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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181 <has_line line="##fileformat=VCFv4.1" />
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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diff changeset
182 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
183 </assert_contents>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
184 </output>
aabb4e1c0b7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
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diff changeset
185 </test>
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
186 </tests>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
187 <help><![CDATA[
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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188 .. class:: infomark
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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diff changeset
189
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
190 **What it does**
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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191
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
192 @WID@
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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193
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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194 The module *variant* decodes probabilities.
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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195
13
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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196 ----
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
197
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
198 .. class:: infomark
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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diff changeset
199
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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200 **Input**
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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201
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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202 - reference sequence (FASTA)
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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203 - (several) consensus files (H5/HDF)
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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204
13
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
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205 ----
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
206
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
207 .. class:: infomark
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
208
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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209 **Output**
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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210
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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211 - decoded probabilities (VCF)
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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212
13
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
213 ----
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
214
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
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215 .. class:: infomark
222669c4afb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 12
diff changeset
216
0
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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217 **References**
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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218
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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219 @REFERENCES@
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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220 ]]></help>
3cde72a6e37c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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221 <expand macro="citations"/>
3
e86fcef8ed91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
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222 </tool>