Mercurial > repos > iuc > bcftools_plugin_frameshifts

comparison bcftools_plugin_frameshifts.xml @ 25:7c7cf05cdb1e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:47:59 +0000
parents 5bd73b287e3b
children
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equal deleted inserted replaced
24:5bd73b287e3b 25:7c7cf05cdb1e
7 </macros> 7 </macros>
8 <expand macro="bio_tools" /> 8 <expand macro="bio_tools" />
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@ 12 @PREPARE_INPUT_FILE@
14 #set $section = $sec_restrict 13 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@ 14 @PREPARE_TARGETS_FILE@
16 @PREPARE_REGIONS_FILE@ 15 @PREPARE_REGIONS_FILE@
17 ## exons file needs to be bgzip and have tabix index 16 ## exons file needs to be bgzip and have tabix index
39 <inputs> 38 <inputs>
40 <expand macro="macro_input" /> 39 <expand macro="macro_input" />
41 <param name="exons" type="data" format="bed" 40 <param name="exons" type="data" format="bed"
42 label="Exons File" help="BED file describing exons" /> 41 label="Exons File" help="BED file describing exons" />
43 <section name="sec_restrict" expanded="false" title="Restrict to"> 42 <section name="sec_restrict" expanded="false" title="Restrict to">
44 <expand macro="macro_restrict" /> 43 <expand macro="macro_region_restrict" />
45 <expand macro="macro_restrict" type="target" label_type="Target" /> 44 <expand macro="macro_target_restrict" />
46 <expand macro="macro_include" /> 45 <expand macro="macro_include" />
47 <expand macro="macro_exclude" /> 46 <expand macro="macro_exclude" />
48 </section> 47 </section>
49 <expand macro="macro_select_output_type" /> 48 <expand macro="macro_select_output_type" />
50 </inputs> 49 </inputs>
57 <param name="exons" ftype="bed" value="plugin_frameshifts.bed" /> 56 <param name="exons" ftype="bed" value="plugin_frameshifts.bed" />
58 <param name="output_type" value="v" /> 57 <param name="output_type" value="v" />
59 <output name="output_file" ftype="vcf"> 58 <output name="output_file" ftype="vcf">
60 <assert_contents> 59 <assert_contents>
61 <has_line_matching expression="##INFO=&lt;ID=OOF,.+" /> 60 <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
62 <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" /> 61 <has_line_matching expression="1\t3106154\t.\tCAAA\tC\t342\tPASS\tOOF=-1.+"/>
63 <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
64 </assert_contents> 62 </assert_contents>
65 </output> 63 </output>
66 </test> 64 </test>
67 </tests> 65 </tests>
68 <help><![CDATA[ 66 <help><![CDATA[