Mercurial > repos > iuc > bcftools_plugin_fixploidy

comparison bcftools_plugin_fixploidy.xml @ 25:adb1d6cb6568 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:54:23 +0000
parents 5d8dc10d436c
children
comparison
equal deleted inserted replaced
24:5d8dc10d436c 25:adb1d6cb6568
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
43 ]]> 42 ]]>
44 </command> 43 </command>
45 <inputs> 44 <inputs>
46 <expand macro="macro_input" /> 45 <expand macro="macro_input" />
47 <section name="sec_restrict" expanded="false" title="Restrict to"> 46 <section name="sec_restrict" expanded="false" title="Restrict to">
48 <expand macro="macro_restrict" /> 47 <expand macro="macro_region_restrict" />
49 <expand macro="macro_restrict" type="target" label_type="Target" /> 48 <expand macro="macro_target_restrict" />
50 <expand macro="macro_include" /> 49 <expand macro="macro_include" />
51 <expand macro="macro_exclude" /> 50 <expand macro="macro_exclude" />
52 </section> 51 </section>
53 <section name="sec_plugin" expanded="true" title="Plugin Options"> 52 <section name="sec_plugin" expanded="true" title="Plugin Options">
54 <expand macro="macro_ploidy_file" /> 53 <expand macro="macro_ploidy_file" />
61 <expand macro="macro_vcf_output" /> 60 <expand macro="macro_vcf_output" />
62 </outputs> 61 </outputs>
63 <tests> 62 <tests>
64 <test> 63 <test>
65 <param name="input_file" ftype="vcf" value="fixploidy.vcf" /> 64 <param name="input_file" ftype="vcf" value="fixploidy.vcf" />
66 <param name="sex" ftype="tabular" value="fixploidy.samples" /> 65 <section name="sec_plugin">
67 <param name="ploidy_file" ftype="tabular" value="fixploidy.ploidy" /> 66 <param name="sex" ftype="tabular" value="fixploidy.samples" />
67 <param name="ploidy_file" ftype="tabular" value="fixploidy.ploidy" />
68 </section>
68 <param name="output_type" value="v" /> 69 <param name="output_type" value="v" />
69 <output name="output_file"> 70 <output name="output_file">
70 <assert_contents> 71 <assert_contents>
71 <has_text_matching expression="3000004\txx\tC\tCTTTT\t11\tq11\tFLAG;IINT=11;IFLT=1.1;ISTR=xxx\tGT:FINT:FFLT:FSTR\t0/0/0/0/0/0:11:1.1:x\t0/0/0/0/0/0/0:11:1.1:xxx\t0|0|0|0|0|0|0|0:11:1.1:xxx" /> 72 <has_text_matching expression="3000004\txx\tC\tCTTTT\t11\tq11\tFLAG;IINT=11;IFLT=1.1;ISTR=xxx\tGT:FINT:FFLT:FSTR\t0/0/0/0/0/0:11:1.1:x\t0/0/0/0/0/0/0:11:1.1:xxx\t0|0|0|0|0|0|0|0:11:1.1:xxx" />
72 </assert_contents> 73 </assert_contents>