Mercurial > repos > iuc > bcftools_plugin_split_vep

comparison bcftools_plugin_split_vep.xml @ 8:3c6c2935919d 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 08:02:40 +0000
parents 553c14ea339c
children
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7:553c14ea339c 8:3c6c2935919d
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 16
49 <param argument="-d" type="boolean" label="Enable Output per transcript/allele consequences on a new line rather rather than as comma-separated fields on a single line" truevalue="-d" falsevalue="" /> 48 <param argument="-d" type="boolean" label="Enable Output per transcript/allele consequences on a new line rather rather than as comma-separated fields on a single line" truevalue="-d" falsevalue="" />
50 <param argument="-p" type="text" optional="true" label="Enter prefix of INFO annotations to be created after splitting the CSQ string (optional)" /> 49 <param argument="-p" type="text" optional="true" label="Enter prefix of INFO annotations to be created after splitting the CSQ string (optional)" />
51 <param argument="-s" type="text" optional="true" label="Select transcripts to extract by type and/or consequence (optional)" help="Argument has the form TR:CSQ. TR = transcript: worst,primary,all (default: all). CSQ = consequence: any,missense,missense+,etc (default: any). Examples can be found in the tool help." /> 50 <param argument="-s" type="text" optional="true" label="Select transcripts to extract by type and/or consequence (optional)" help="Argument has the form TR:CSQ. TR = transcript: worst,primary,all (default: all). CSQ = consequence: any,missense,missense+,etc (default: any). Examples can be found in the tool help." />
52 <param argument="--allow-undef-tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" checked="false" label="Allow undefined tags" help='Print "." for undefined tags' /> 51 <param argument="--allow-undef-tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" checked="false" label="Allow undefined tags" help='Print "." for undefined tags' />
53 <section name="sec_restrict" expanded="false" title="Restrict to"> 52 <section name="sec_restrict" expanded="false" title="Restrict to">
54 <expand macro="macro_restrict" /> 53 <expand macro="macro_region_restrict" />
55 <expand macro="macro_restrict" type="target" label_type="Target" /> 54 <expand macro="macro_target_restrict" />
56 <expand macro="macro_include" /> 55 <expand macro="macro_include" />
57 <expand macro="macro_exclude" /> 56 <expand macro="macro_exclude" />
58 </section> 57 </section>
59 <expand macro="macro_select_output_type" /> 58 <expand macro="macro_select_output_type" />
60 </inputs> 59 </inputs>