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comparison bcftools_csq.xml @ 3:40388f544e5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:09:13 -0400
parents 039ea3f1dea9
children f10f5b4e7854
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equal deleted inserted replaced
2:039ea3f1dea9 3:40388f544e5d
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
3 <description>Haplotype aware consequence predictor</description> 3 <description>Haplotype aware consequence predictor</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">csq</token> 5 <token name="@EXECUTABLE@">csq</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
10 </expand> 10 </expand>
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 14 @PREPARE_INPUT_FILE@
15 #set $section = $sec_required 15 #set $section = $sec_required.reference_source
16 @PREPARE_FASTA_REF@ 16 @PREPARE_FASTA_REF@
17 17
18 #set $section = $sec_restrict 18 #set $section = $sec_restrict
19 @PREPARE_TARGETS_FILE@ 19 @PREPARE_TARGETS_FILE@
20 @PREPARE_REGIONS_FILE@ 20 @PREPARE_REGIONS_FILE@
21 21
22 bcftools @EXECUTABLE@ 22 bcftools @EXECUTABLE@
23 23
24 ## csq required inputs section 24 ## csq required inputs section
25 #set $section = $sec_required 25 #set $section = $sec_required.reference_source
26 @FASTA_REF@ 26 @FASTA_REF@
27 --gff-annot '$section.gff_annot' 27 --gff-annot '$sec_required.gff_annot'
28 28
29 ## csq options section 29 ## csq options section
30 #set $section = $sec_csq_opts 30 #if str($sec_csq_opts.ncsq):
31 #if str($section.ncsq): 31 --ncsq $sec_csq_opts.ncsq
32 --ncsq $section.ncsq
33 #end if 32 #end if
34 $section.local_csq 33 $sec_csq_opts.local_csq
35 #if $section.phase: 34 #if $sec_csq_opts.phase:
36 --phase $section.phase 35 --phase $sec_csq_opts.phase
37 #end if 36 #end if
38 #if str($section.custom_tag): 37 #if str($sec_csq_opts.custom_tag):
39 --custom-tag '$section.custom_tag' 38 --custom-tag '$sec_csq_opts.custom_tag'
40 #end if 39 #end if
41 40
42 ## Subset section 41 ## Subset section
43 #set $section = $sec_subset 42 #set $section = $sec_subset
44 @SAMPLES@ 43 @SAMPLES@
83 <validator type="regex" message="">^(\w+)?$</validator> 82 <validator type="regex" message="">^(\w+)?$</validator>
84 </param> 83 </param>
85 </section> 84 </section>
86 85
87 <section name="sec_restrict" expanded="false" title="Restrict to"> 86 <section name="sec_restrict" expanded="false" title="Restrict to">
88 <expand macro="macro_regions" /> 87 <expand macro="macro_restrict" />
89 <expand macro="macro_targets" /> 88 <expand macro="macro_restrict" type="target" label_type="Target" />
90 <expand macro="macro_include" /> 89 <expand macro="macro_include" />
91 <expand macro="macro_exclude" /> 90 <expand macro="macro_exclude" />
92 </section> 91 </section>
93 <section name="sec_subset" expanded="false" title="Subset Options"> 92 <section name="sec_subset" expanded="false" title="Subset Options">
94 <expand macro="macro_samples" /> 93 <expand macro="macro_samples" />
99 <expand macro="macro_vcf_output" /> 98 <expand macro="macro_vcf_output" />
100 </outputs> 99 </outputs>
101 <tests> 100 <tests>
102 <test> 101 <test>
103 <param name="input_file" ftype="vcf" value="csq.vcf" /> 102 <param name="input_file" ftype="vcf" value="csq.vcf" />
104 <param name="fasta_ref" ftype="fasta" value="csq.fa" /> 103 <expand macro="test_using_reference" ref="csq.fa" />
105 <param name="gff_annot" ftype="gff3" value="csq.gff3" /> 104 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
106 <param name="output_type" value="v" /> 105 <param name="output_type" value="v" />
107 <output name="output_file"> 106 <output name="output_file">
108 <assert_contents> 107 <assert_contents>
109 <has_text text="BCSQ" /> 108 <has_text text="BCSQ" />
110 </assert_contents> 109 </assert_contents>
111 </output> 110 </output>
112 </test> 111 </test>
112 <test>
113 <param name="input_file" ftype="vcf" dbkey="?" value="csq.vcf" />
114 <expand macro="test_using_reference" select_from="cached" ref="csq" />
115 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
116 <param name="output_type" value="v" />
117 <output name="output_file">
118 <assert_contents>
119 <has_text text="BCSQ" />
120 </assert_contents>
121 </output>
122 </test>
123
113 </tests> 124 </tests>
114 <help><![CDATA[ 125 <help><![CDATA[
115 ===================================== 126 =====================================
116 bcftools @EXECUTABLE@ 127 bcftools @EXECUTABLE@
117 ===================================== 128 =====================================