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comparison 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
comparison
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2:cb0285133e29 3:009673c8ac31
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>Probability decoding</description> 3 <description>Probability decoding</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
23 #for $current in $inputs 23 #for $current in $inputs
24 '$current' 24 '$current'
25 #end for 25 #end for
26 '$out_result' ## output 26 '$out_result' ## output
27 27
28 |& tee '$out_log' 28 2>&1 | tee '$out_log'
29
30 #if $out_annotated
31 && python '$__tool_directory__/annotateVCF.py' '$out_result' '$in_mpileup' '$out_annotated'
32 #end if
29 ]]></command> 33 ]]></command>
30 <inputs> 34 <inputs>
31 <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/> 35 <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
32 <expand macro="reference"/> 36 <expand macro="reference"/>
33 <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','."/> 37 <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','.">
38 <sanitizer invalid_char="">
39 <valid initial="string.ascii_letters,string.digits">
40 <add value="_"/>
41 <add value=","/>
42 <add value="."/>
43 </valid>
44 </sanitizer>
45 </param>
34 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/> 46 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
35 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> 47
36 <option value="result" selected="true">Result</option> 48 <conditional name="output_annotated">
37 <option value="log">Log</option> 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)">
38 </param> 50 <option value="true" selected="true">Output annotated VCF</option>
51 <option value="false">Don't output annotated VCF</option>
52 </param>
53 <when value="true">
54 <param name="in_mpileup" type = "data" format="pileup" optional="false" label="Mpileup to annotate the VCF"/>
55 </when>
56 </conditional>
57 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
39 </inputs> 58 </inputs>
40 <outputs> 59 <outputs>
41 <!-- standard --> 60 <!-- standard -->
42 <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"> 61 <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/>
43 <filter>'result' in out</filter> 62 <!-- optional -->
63 <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated">
64 <filter>output_annotated_select</filter>
44 </data> 65 </data>
45 <!-- optional -->
46 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log"> 66 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
47 <filter>'log' in out</filter> 67 <filter>output_log_bool</filter>
48 </data> 68 </data>
49 </outputs> 69 </outputs>
50 <tests> 70 <tests>
51 <!-- #1 default --> 71 <!-- #1 default -->
52 <test expect_num_outputs="1"> 72 <test expect_num_outputs="3">
73 <param name="inputs" value="medaka_test.hdf"/>
53 <conditional name="reference_source"> 74 <conditional name="reference_source">
54 <param name="reference_source_selector" value="cached"/> 75 <param name="reference_source_selector" value="history"/>
55 <param name="ref_file" value="bwa-mem-mt-genome"/> 76 <param name="ref_file" value="ref.fasta"/>
56 </conditional> 77 </conditional>
57 <param name="inputs" value="consensus.hdf"/> 78 <conditional name="output_annotated">
79 <param name="output_annotated_select" value="true"/>
80 <param name="in_mpileup" value="annotate_vcf_test.pileup"/>
81 </conditional>
82 <param name="output_log_bool" value="true"/>
83
58 <output name="out_result"> 84 <output name="out_result">
59 <assert_contents> 85 <assert_contents>
60 <has_n_lines n="6"/> 86 <has_n_lines n="9"/>
61 <has_line line="##fileformat=VCFv4.1"/> 87 <has_line line="##fileformat=VCFv4.1" />
88 <has_line line="##medaka_version=1.0.3" />
62 </assert_contents> 89 </assert_contents>
63 </output> 90 </output>
64 </test> 91 <output name="out_annotated">
65 <!-- #2 -->
66 <test expect_num_outputs="2">
67 <conditional name="reference_source">
68 <param name="reference_source_selector" value="cached"/>
69 <param name="ref_file" value="bwa-mem-mt-genome"/>
70 </conditional>
71 <param name="inputs" value="consensus.hdf"/>
72 <param name="verbose" value="true"/>
73 <param name="out" value="result,log"/>
74 <output name="out_result">
75 <assert_contents> 92 <assert_contents>
76 <has_n_lines n="13"/> 93 <has_n_lines n="16"/>
77 <has_line line="##fileformat=VCFv4.1"/> 94 <has_line line="##fileformat=VCFv4.1" />
95 <has_line line="##medaka_version=1.0.3" />
96 <has_line line="##annotateVCFVersion=0.1" />
78 </assert_contents> 97 </assert_contents>
79 </output> 98 </output>
80 <output name="out_log"> 99 <output name="out_log">
81 <assert_contents> 100 <assert_contents>
82 <has_n_lines n="17"/> 101 <has_n_lines n="8" />
83 <has_text_matching expression=".+Loaded.+"/>
84 </assert_contents> 102 </assert_contents>
85 </output> 103 </output>
86 </test> 104 </test>
87 </tests> 105 </tests>
88 <help><![CDATA[ 106 <help><![CDATA[