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comparison bcftools_csq.xml @ 13:aed58f2684fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:40:48 +0000
parents 6014ca4c359f
children 10da4a86ee5c
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12:530767e7c5d1 13:aed58f2684fe
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@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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>
35 #if $sec_csq_opts.phase: 35 #if $sec_csq_opts.phase:
36 --phase $sec_csq_opts.phase 36 --phase $sec_csq_opts.phase
37 #end if 37 #end if
38 #if str($sec_csq_opts.custom_tag): 38 #if str($sec_csq_opts.custom_tag):
39 --custom-tag '$sec_csq_opts.custom_tag' 39 --custom-tag '$sec_csq_opts.custom_tag'
40 #end if
41 #if str($sec_csq_opts.trim_protein_seq)
42 --trim-protein-seq $sec_csq_opts.trim_protein_seq
40 #end if 43 #end if
41 44
42 ## Subset section 45 ## Subset section
43 #set $section = $sec_subset 46 #set $section = $sec_subset
44 @SAMPLES@ 47 @SAMPLES@
80 </param> 83 </param>
81 <param name="custom_tag" type="text" value="" optional="true" 84 <param name="custom_tag" type="text" value="" optional="true"
82 label="use this custom tag to store consequences rather than the default BCSQ tag"> 85 label="use this custom tag to store consequences rather than the default BCSQ tag">
83 <validator type="regex" message="">^(\w+)?$</validator> 86 <validator type="regex" message="">^(\w+)?$</validator>
84 </param> 87 </param>
88 <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions"
89 help="Abbreviate protein-changing predictions to max INT aminoacids" />
85 </section> 90 </section>
86 91
87 <section name="sec_restrict" expanded="false" title="Restrict to"> 92 <section name="sec_restrict" expanded="false" title="Restrict to">
88 <expand macro="macro_restrict" /> 93 <expand macro="macro_restrict" />
89 <expand macro="macro_restrict" type="target" label_type="Target" /> 94 <expand macro="macro_restrict" type="target" label_type="Target" />
109 <has_text text="BCSQ" /> 114 <has_text text="BCSQ" />
110 </assert_contents> 115 </assert_contents>
111 </output> 116 </output>
112 </test> 117 </test>
113 <test> 118 <test>
114 <param name="input_file" ftype="vcf" dbkey="?" value="csq.vcf" /> 119 <param name="input_file" ftype="vcf" value="csq.vcf" />
115 <expand macro="test_using_reference" select_from="cached" ref="csq" /> 120 <expand macro="test_using_reference" select_from="cached" ref="csq" />
116 <param name="gff_annot" ftype="gff3" value="csq.gff3" /> 121 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
117 <param name="output_type" value="v" /> 122 <param name="output_type" value="v" />
118 <output name="output_file"> 123 <output name="output_file">
119 <assert_contents> 124 <assert_contents>
120 <has_text text="BCSQ" /> 125 <has_text text="BCSQ" />
121 </assert_contents> 126 </assert_contents>
122 </output> 127 </output>
123 </test> 128 </test>
124 129 <!-- Test protein seq prediction-->
130 <test>
131 <param name="input_file" ftype="vcf" value="csq.vcf" />
132 <expand macro="test_using_reference" select_from="cached" ref="csq" />
133 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
134 <param name="output_type" value="v" />
135 <section name="sec_csq_opts">
136 <param name="trim_protein_seq" value="10"/>
137 </section>
138 <output name="output_file">
139 <assert_contents>
140 <has_text text="BCSQ" />
141 </assert_contents>
142 </output>
143 <assert_command>
144 <has_text text="--trim-protein-seq" />
145 </assert_command>
146 </test>
147 <!-- Test region overlap-->
148 <test>
149 <param name="input_file" ftype="vcf" value="csq.vcf" />
150 <expand macro="test_using_reference" select_from="cached" ref="csq" />
151 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
152 <param name="output_type" value="v" />
153 <section name="sec_restrict">
154 <param name="regions_overlap" value="1"/>
155 </section>
156 <output name="output_file">
157 <assert_contents>
158 <has_text text="BCSQ" />
159 </assert_contents>
160 </output>
161 <assert_command>
162 <has_text text="--regions-overlap" />
163 </assert_command>
164 </test>
125 </tests> 165 </tests>
126 <help><![CDATA[ 166 <help><![CDATA[
127 ===================================== 167 =====================================
128 bcftools @EXECUTABLE@ 168 bcftools @EXECUTABLE@
129 ===================================== 169 =====================================