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comparison samtools_phase.xml @ 8:54bbc447e348 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_phase commit 8d2369dc1bdafc743920a155c508c20114ebe655
author iuc
date Mon, 17 Nov 2025 07:30:17 +0000
parents 2504000d5158
children
comparison
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7:2504000d5158 8:54bbc447e348
1 <tool id="samtools_phase" name="Samtools phase" version="2.0.2" profile="@PROFILE@"> 1 <tool id="samtools_phase" name="Samtools phase" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>call and phase heterozygous SNPs</description> 2 <description>call and phase heterozygous SNPs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
46 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" /> 46 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
47 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" /> 47 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
48 <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" /> 48 <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
49 </outputs> 49 </outputs>
50 <tests> 50 <tests>
51 <!-- 1) -->
51 <test> 52 <test>
52 <param name="option_sets" value="default" /> 53 <conditional name="option_set">
54 <param name="option_sets" value="default" />
55 </conditional>
53 <param name="input_bam" value="samtools_phase_in_1.bam" /> 56 <param name="input_bam" value="samtools_phase_in_1.bam" />
54 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" /> 57 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt">
55 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" lines_diff="4" /> 58 <assert_contents>
56 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" lines_diff="4" /> 59 <has_text_matching expression="Descriptions:"/>
57 <output name="chimera" file="empty_file_1.bam" ftype="bam" lines_diff="4" /> 60 </assert_contents>
61 </output>
62 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" compare="sim_size"/>
63 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" compare="sim_size"/>
64 <output name="chimera" file="empty_file_1.bam" ftype="bam" compare="sim_size"/>
58 </test> 65 </test>
66 <!-- 2) -->
59 <test> 67 <test>
60 <param name="input_bam" value="samtools_phase_in_2.bam" /> 68 <param name="input_bam" value="samtools_phase_in_2.bam" />
61 <param name="option_sets" value="advanced" /> 69 <conditional name="option_set">
70 <param name="option_sets" value="advanced" />
71 </conditional>
62 <param name="option_set|block_length" value="13" /> 72 <param name="option_set|block_length" value="13" />
63 <param name="option_set|min_het" value="37" /> 73 <param name="option_set|min_het" value="37" />
64 <param name="option_set|min_bq" value="13" /> 74 <param name="option_set|min_bq" value="13" />
65 <param name="option_set|read_depth" value="256" /> 75 <param name="option_set|read_depth" value="256" />
66 <param name="option_set|ignore_chimeras" value="false" /> 76 <param name="option_set|ignore_chimeras" value="false" />
67 <param name="option_set|drop_ambiguous" value="true" /> 77 <param name="option_set|drop_ambiguous" value="true" />
68 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" /> 78 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt">
69 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" lines_diff="4" /> 79 <assert_contents>
70 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" lines_diff="4" /> 80 <has_text_matching expression="Descriptions:"/>
71 <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" lines_diff="4" /> 81 </assert_contents>
82 </output>
83 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" compare="sim_size"/>
84 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" compare="sim_size"/>
85 <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" compare="sim_size"/>
72 </test> 86 </test>
87 <!-- 3) -->
73 <test> 88 <test>
74 <param name="input_bam" value="samtools_phase_in_2.bam" /> 89 <param name="input_bam" value="samtools_phase_in_2.bam" />
75 <param name="option_sets" value="advanced" /> 90 <conditional name="option_set">
91 <param name="option_sets" value="advanced" />
92 </conditional>
76 <param name="option_set|block_length" value="13" /> 93 <param name="option_set|block_length" value="13" />
77 <param name="option_set|min_het" value="37" /> 94 <param name="option_set|min_het" value="37" />
78 <param name="option_set|min_bq" value="13" /> 95 <param name="option_set|min_bq" value="13" />
79 <param name="option_set|read_depth" value="256" /> 96 <param name="option_set|read_depth" value="256" />
80 <param name="option_set|ignore_chimeras" value="true" /> 97 <param name="option_set|ignore_chimeras" value="true" />
81 <param name="option_set|drop_ambiguous" value="false" /> 98 <param name="option_set|drop_ambiguous" value="false" />
82 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" /> 99 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt">
83 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" lines_diff="4" /> 100 <assert_contents>
84 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" lines_diff="4" /> 101 <has_text_matching expression="Descriptions:"/>
85 <output name="chimera" file="empty_file_3.bam" ftype="bam" lines_diff="4" /> 102 </assert_contents>
103 </output>
104 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" compare="sim_size"/>
105 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" compare="sim_size"/>
106 <output name="chimera" file="empty_file_3.bam" ftype="bam" compare="sim_size"/>
86 </test> 107 </test>
87 </tests> 108 </tests>
88 <help><![CDATA[ 109 <help><![CDATA[
89 **What it does** 110 **What it does**
90 111