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comparison samtools_phase.xml @ 4:1e5880498f52 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:15:54 +0000
parents b5c3b1856370
children
comparison
equal deleted inserted replaced
3:b5c3b1856370 4:1e5880498f52
1 <tool id="samtools_phase" name="Call and phase" version="2.0.1"> 1 <tool id="samtools_phase" name="Samtools phase" version="2.0.2" profile="@PROFILE@">
2 <description>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"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
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 <test> 51 <test>
52 <param name="option_sets" value="default" /> 52 <param name="option_sets" value="default" />
53 <param name="input_bam" value="samtools_phase_in_1.bam" /> 53 <param name="input_bam" value="samtools_phase_in_1.bam" />
54 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" /> 54 <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" /> 55 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" lines_diff="4" />
56 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" /> 56 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" lines_diff="4" />
57 <output name="chimera" file="empty_file.bam" ftype="bam" /> 57 <output name="chimera" file="empty_file_1.bam" ftype="bam" lines_diff="4" />
58 </test> 58 </test>
59 <test> 59 <test>
60 <param name="input_bam" value="samtools_phase_in_2.bam" /> 60 <param name="input_bam" value="samtools_phase_in_2.bam" />
61 <param name="option_sets" value="advanced" /> 61 <param name="option_sets" value="advanced" />
62 <param name="option_set|block_length" value="13" /> 62 <param name="option_set|block_length" value="13" />
63 <param name="option_set|min_het" value="37" /> 63 <param name="option_set|min_het" value="37" />
64 <param name="option_set|min_bq" value="13" /> 64 <param name="option_set|min_bq" value="13" />
65 <param name="option_set|read_depth" value="256" /> 65 <param name="option_set|read_depth" value="256" />
66 <param name="option_set|ignore_chimeras" value="false" /> 66 <param name="option_set|ignore_chimeras" value="false" />
67 <param name="option_set|drop_ambiguous" value="true" /> 67 <param name="option_set|drop_ambiguous" value="true" />
68 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" /> 68 <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" /> 69 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" lines_diff="4" />
70 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" /> 70 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" lines_diff="4" />
71 <output name="chimera" file="samtools_phase_out_2_chimera.bam" /> 71 <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" lines_diff="4" />
72 </test> 72 </test>
73 <test> 73 <test>
74 <param name="input_bam" value="samtools_phase_in_2.bam" /> 74 <param name="input_bam" value="samtools_phase_in_2.bam" />
75 <param name="option_sets" value="advanced" /> 75 <param name="option_sets" value="advanced" />
76 <param name="option_set|block_length" value="13" /> 76 <param name="option_set|block_length" value="13" />
77 <param name="option_set|min_het" value="37" /> 77 <param name="option_set|min_het" value="37" />
78 <param name="option_set|min_bq" value="13" /> 78 <param name="option_set|min_bq" value="13" />
79 <param name="option_set|read_depth" value="256" /> 79 <param name="option_set|read_depth" value="256" />
80 <param name="option_set|ignore_chimeras" value="true" /> 80 <param name="option_set|ignore_chimeras" value="true" />
81 <param name="option_set|drop_ambiguous" value="false" /> 81 <param name="option_set|drop_ambiguous" value="false" />
82 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" /> 82 <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" /> 83 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" lines_diff="4" />
84 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" /> 84 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" lines_diff="4" />
85 <output name="chimera" file="empty_file.bam"/> 85 <output name="chimera" file="empty_file_3.bam" ftype="bam" lines_diff="4" />
86 </test> 86 </test>
87 </tests> 87 </tests>
88 <help><![CDATA[ 88 <help><![CDATA[
89 **What it does** 89 **What it does**
90 90