comparison samtools_phase.xml @ 6:dd8305e4e58e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty
author iuc
date Sun, 28 Jul 2019 14:49:27 -0400
parents 2311187710fb
children 2504000d5158
comparison
equal deleted inserted replaced
5:2311187710fb 6:dd8305e4e58e
35 <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" /> 35 <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
36 <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> 36 <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
37 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" /> 37 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
38 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" /> 38 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
39 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> 39 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
40 <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> 40 <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
41 </when> 41 </when>
42 </conditional> 42 </conditional>
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <data format="txt" name="phase_sets" /> 45 <data format="txt" name="phase_sets" />
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 ${on_string}: Phase-1 reads" />
48 <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${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" />
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" />
57 <output name="chimera" file="empty_file.bam" compare="contains" /> 57 <output name="chimera" file="empty_file.bam" ftype="bam" />
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" />
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" />
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" />
71 <output name="chimera" file="empty_file.bam" compare="contains" /> 71 <output name="chimera" file="samtools_phase_out_2_chimera.bam" />
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" />
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" />
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" />
85 <output name="chimera" file="empty_file.bam" compare="contains" /> 85 <output name="chimera" file="empty_file.bam"/>
86 </test> 86 </test>
87 </tests> 87 </tests>
88 <help><![CDATA[ 88 <help><![CDATA[
89 **What it does** 89 **What it does**
90 90