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comparison vcffilter.xml @ 8:81972652519c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
author iuc
date Tue, 07 May 2019 12:01:04 -0400
parents eae7c08ebb6f
children fa24bf0598f4
comparison
equal deleted inserted replaced
7:eae7c08ebb6f 8:81972652519c
1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2"> 1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy3">
2 <description>filter VCF data in a variety of attributes</description> 2 <description>filter VCF data in a variety of attributes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
33 <repeat name="filter_repeat" title="more filters" min="1"> 33 <repeat name="filter_repeat" title="more filters" min="1">
34 <param name="filter_type" type="select" label="Select the filter type"> 34 <param name="filter_type" type="select" label="Select the filter type">
35 <option value="-f">Info filter (-f)</option> 35 <option value="-f">Info filter (-f)</option>
36 <option value="-g">Genotype filter (-g)</option> 36 <option value="-g">Genotype filter (-g)</option>
37 </param> 37 </param>
38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below"> 38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filtering value" help="See explanation of filtering options below">
39 <sanitizer> 39 <sanitizer>
40 <valid initial="string.printable"> 40 <valid initial="string.printable">
41 <remove value="&apos;"/> 41 <remove value="&apos;"/>
42 <remove value="&quot;"/> 42 <remove value="&quot;"/>
43 </valid> 43 </valid>
44 <mapping initial="none"> 44 <mapping initial="none">
45 <add source="&apos;" target=""/> 45 <add source="&apos;" target=""/>
46 <add source="&quot;" target=""/> 46 <add source="&quot;" target=""/>
47 </mapping> 47 </mapping>
48 </sanitizer> 48 </sanitizer>
49 <validator type="expression" message="Invalid operator provided, valid operators are =, !, &lt;, &gt;, |, &amp;.">value is not None and not any(x in value for x in ["&lt;=", "=&lt;", "&gt;=", "=&gt;"])</validator>
49 </param> 50 </param>
50 </repeat> 51 </repeat>
51 <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/> 52 <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
52 <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/> 53 <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
53 <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/> 54 <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>
64 <test> 65 <test>
65 <param name="filter_repeat_0|filter_type" value="-f"/> 66 <param name="filter_repeat_0|filter_type" value="-f"/>
66 <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/> 67 <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/>
67 <param name="input1" value="vcflib.vcf"/> 68 <param name="input1" value="vcflib.vcf"/>
68 <output name="out_file1" file="vcffilter-test1.vcf"/> 69 <output name="out_file1" file="vcffilter-test1.vcf"/>
70 </test>
71 <test>
72 <param name="filter_repeat_0|filter_type" value="-f"/>
73 <param name="filter_repeat_0|filter_value" value="!( DP &gt; 10 )"/>
74 <param name="invert" value="true"/>
75 <param name="input1" value="vcflib.vcf"/>
76 <output name="out_file1" file="vcffilter-test2.vcf"/>
69 </test> 77 </test>
70 </tests> 78 </tests>
71 <help><![CDATA[ 79 <help><![CDATA[
72 You can specify the following options within the **Specify filtering expression** box in any combination:: 80 You can specify the following options within the **Specify filtering expression** box in any combination::
73 81