Mercurial > repos > iuc > bcftools_query
comparison bcftools_query.xml @ 23:1dc6f1ac7f32 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
| author | iuc |
|---|---|
| date | Tue, 02 Dec 2025 08:06:21 +0000 |
| parents | 31a1b89eab9b |
| children |
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| 22:31a1b89eab9b | 23:1dc6f1ac7f32 |
|---|---|
| 6 </macros> | 6 </macros> |
| 7 <expand macro="bio_tools" /> | 7 <expand macro="bio_tools" /> |
| 8 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
| 9 <expand macro="version_command" /> | 9 <expand macro="version_command" /> |
| 10 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
| 11 @PREPARE_ENV@ | |
| 12 @PREPARE_INPUT_FILES@ | 11 @PREPARE_INPUT_FILES@ |
| 13 #set $section = $sec_restrict | 12 #set $section = $sec_restrict |
| 14 @PREPARE_TARGETS_FILE@ | 13 @PREPARE_TARGETS_FILE@ |
| 15 @PREPARE_REGIONS_FILE@ | 14 @PREPARE_REGIONS_FILE@ |
| 16 | 15 |
| 41 <inputs> | 40 <inputs> |
| 42 <expand macro="macro_inputs" /> | 41 <expand macro="macro_inputs" /> |
| 43 <section name="sec_restrict" expanded="false" title="Restrict to"> | 42 <section name="sec_restrict" expanded="false" title="Restrict to"> |
| 44 <expand macro="macro_collapse" /> | 43 <expand macro="macro_collapse" /> |
| 45 <expand macro="macro_samples" /> | 44 <expand macro="macro_samples" /> |
| 46 <expand macro="macro_restrict" /> | 45 <expand macro="macro_region_restrict" /> |
| 47 <expand macro="macro_restrict" type="target" label_type="Target" /> | 46 <expand macro="macro_target_restrict" /> |
| 48 <expand macro="macro_include" /> | 47 <expand macro="macro_include" /> |
| 49 <expand macro="macro_exclude" /> | 48 <expand macro="macro_exclude" /> |
| 50 </section> | 49 </section> |
| 51 <section name="sec_query" expanded="true" title="Query Options"> | 50 <section name="sec_query" expanded="true" title="Query Options"> |
| 52 <param name="format" type="text" value="" label="Format for Output"> | 51 <param name="format" type="text" value="" label="Format for Output"> |
| 75 </data> | 74 </data> |
| 76 </outputs> | 75 </outputs> |
| 77 <tests> | 76 <tests> |
| 78 <test> | 77 <test> |
| 79 <param name="input_files" ftype="vcf" value="query.vcf" /> | 78 <param name="input_files" ftype="vcf" value="query.vcf" /> |
| 80 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> | 79 <section name="sec_query"> |
| 81 <param name="tsv" value="True" /> | 80 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> |
| 81 <param name="tsv" value="True" /> | |
| 82 </section> | |
| 82 <output name="output_file" file="query.out" /> | 83 <output name="output_file" file="query.out" /> |
| 83 </test> | 84 </test> |
| 84 <!-- Test region overlap option--> | 85 <!-- Test region overlap option--> |
| 85 <test> | 86 <test> |
| 86 <param name="input_files" ftype="vcf" value="query.vcf" /> | 87 <param name="input_files" ftype="vcf" value="query.vcf" /> |
| 87 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> | 88 <section name="sec_query"> |
| 88 <param name="tsv" value="True" /> | 89 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> |
| 90 <param name="tsv" value="True" /> | |
| 91 </section> | |
| 89 <section name="sec_restrict"> | 92 <section name="sec_restrict"> |
| 90 <param name="regions_overlap" value="1"/> | 93 <conditional name="regions"> |
| 94 <param name="regions_src" value="regions" /> | |
| 95 <repeat name="region_specs"> | |
| 96 <param name="chrom" value="1" /> | |
| 97 </repeat> | |
| 98 </conditional> | |
| 91 </section> | 99 </section> |
| 92 <output name="output_file" file="query.out" /> | 100 <output name="output_file" file="query.out" compare="contains" lines_diff="4"/> |
| 93 <assert_command> | 101 <assert_command> |
| 94 <has_text text="--regions-overlap" /> | 102 <has_text text="--regions-overlap" /> |
| 95 </assert_command> | 103 </assert_command> |
| 96 </test> | 104 </test> |
| 97 </tests> | 105 </tests> |
| 148 @TARGETS_HELP@ | 156 @TARGETS_HELP@ |
| 149 @EXPRESSIONS_HELP@ | 157 @EXPRESSIONS_HELP@ |
| 150 | 158 |
| 151 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ | 159 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
| 152 | 160 |
| 153 @BCFTOOLS_WIKI@ | 161 @BCFTOOLS_HOWTOS@ |
| 154 ]]> | 162 ]]> |
| 155 </help> | 163 </help> |
| 156 <expand macro="citations" /> | 164 <expand macro="citations" /> |
| 157 </tool> | 165 </tool> |