Mercurial > repos > blankenberg > naive_variant_caller
comparison naive_variant_caller.xml @ 16:07e71cf6c8ef draft
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
| author | blankenberg |
|---|---|
| date | Tue, 03 Apr 2018 10:52:11 -0400 |
| parents | aff38ea879f1 |
| children | 6be51647d31a |
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| 15:aff38ea879f1 | 16:07e71cf6c8ef |
|---|---|
| 1 <tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3"> | 1 <tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.4"> |
| 2 <description> - tabulate variable sites from BAM datasets</description> | 2 <description> - tabulate variable sites from BAM datasets</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.0.3">nvc</requirement> | 4 <requirement type="package" version="0.0.4">nvc</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <stdio> | 6 <stdio> |
| 7 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
| 8 <exit_code range=":-1" /> | 8 <exit_code range=":-1" /> |
| 9 </stdio> | 9 </stdio> |
| 101 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" /> | 101 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" /> |
| 102 | 102 |
| 103 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> | 103 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> |
| 104 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/> | 104 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/> |
| 105 | 105 |
| 106 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/> | 106 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="True" label="Report counts by strand"/> |
| 107 | 107 |
| 108 <conditional name="advanced_options"> | 108 <conditional name="advanced_options"> |
| 109 <param name="advanced_options_selector" type="select" label="Show Advanced Options"> | 109 <param name="advanced_options_selector" type="select" label="Show Advanced Options"> |
| 110 <option value="basic" selected="True">Hide Advanced Options</option> | 110 <option value="basic" selected="True">Hide Advanced Options</option> |
| 111 <option value="advanced">Show Advanced Options</option> | 111 <option value="advanced">Show Advanced Options</option> |
| 143 <param name="use_strand" value="False" /> | 143 <param name="use_strand" value="False" /> |
| 144 <param name="advanced_options_selector" value="advanced" /> | 144 <param name="advanced_options_selector" value="advanced" /> |
| 145 <param name="coverage_dtype" value="uint8" /> | 145 <param name="coverage_dtype" value="uint8" /> |
| 146 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" /> | 146 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" /> |
| 147 </test> | 147 </test> |
| 148 <test> | |
| 149 <param name="reference_source_selector" value="history" /> | |
| 150 <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" /> | |
| 151 <param name="ref_file" value="phiX174.fasta" ftype="fasta" /> | |
| 152 <param name="regions" value="0" /> | |
| 153 <param name="min_support_depth" value="0" /> | |
| 154 <param name="min_base_quality" value="" /> | |
| 155 <param name="min_mapping_quality" value="" /> | |
| 156 <param name="ploidy" value="2" /> | |
| 157 <param name="variants_only" value="False" /> | |
| 158 <param name="use_strand" value="True" /> | |
| 159 <param name="advanced_options_selector" value="advanced" /> | |
| 160 <param name="coverage_dtype" value="uint8" /> | |
| 161 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_2.vcf" compare="contains" /> | |
| 162 </test> | |
| 148 </tests> | 163 </tests> |
| 149 <help> | 164 <help> |
| 150 The **Naive Variant Caller** tool (NVC). | 165 The **Naive Variant Caller** tool (NVC). |
| 151 | 166 |
| 152 ------ | 167 ------ |