Mercurial > repos > iuc > vsnp_add_zero_coverage
comparison vsnp_add_zero_coverage.xml @ 7:6dc6dd4666e3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
| author | iuc |
|---|---|
| date | Tue, 16 Nov 2021 20:10:48 +0000 |
| parents | 9ddeef840a07 |
| children | 40b97055bb99 |
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| 6:9ddeef840a07 | 7:6dc6dd4666e3 |
|---|---|
| 1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2+galaxy0" profile="@PROFILE@"> | 1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description></description> | 2 <description></description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 7 <requirement type="package" version="3.0.7">openpyxl</requirement> | 7 <expand macro="biopython_requirement"/> |
| 8 <requirement type="package" version="1.79">biopython</requirement> | 8 <expand macro="openpyxl_requirement"/> |
| 9 <requirement type="package" version="1.3.0">pandas</requirement> | 9 <expand macro="pandas_requirement"/> |
| 10 <requirement type="package" version="0.16.0.1">pysam</requirement> | 10 <requirement type="package" version="0.16.0.1">pysam</requirement> |
| 11 </requirements> | 11 </requirements> |
| 12 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
| 13 #import re | 13 #import re |
| 14 | 14 |
| 56 <test expect_num_outputs="2"> | 56 <test expect_num_outputs="2"> |
| 57 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> | 57 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> |
| 58 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> | 58 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> |
| 59 <param name="reference_source" value="history"/> | 59 <param name="reference_source" value="history"/> |
| 60 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/> | 60 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/> |
| 61 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/> | 61 <output name="output_vcf" ftype="vcf"> |
| 62 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular"/> | 62 <assert_contents> |
| 63 <has_size value="259726"/> | |
| 64 </assert_contents> | |
| 65 </output> | |
| 66 <output name="output_metrics" ftype="tabular"> | |
| 67 <assert_contents> | |
| 68 <has_size value="109"/> | |
| 69 </assert_contents> | |
| 70 </output> | |
| 63 </test> | 71 </test> |
| 64 <test expect_num_outputs="2"> | 72 <test expect_num_outputs="2"> |
| 65 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> | 73 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> |
| 66 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> | 74 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> |
| 67 <param name="reference_source" value="cached"/> | 75 <param name="reference_source" value="cached"/> |
| 68 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/> | 76 <output name="output_vcf" ftype="vcf"> |
| 69 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular" compare="contains"/> | 77 <assert_contents> |
| 78 <has_size value="259726"/> | |
| 79 </assert_contents> | |
| 80 </output> | |
| 81 <output name="output_metrics" ftype="tabular"> | |
| 82 <assert_contents> | |
| 83 <has_size value="109"/> | |
| 84 </assert_contents> | |
| 85 </output> | |
| 70 </test> | 86 </test> |
| 71 </tests> | 87 </tests> |
| 72 <help> | 88 <help> |
| 73 **What it does** | 89 **What it does** |
| 74 | 90 |
| 81 | 97 |
| 82 **Required Options** | 98 **Required Options** |
| 83 | 99 |
| 84 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history. | 100 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history. |
| 85 </help> | 101 </help> |
| 86 <expand macro="citations" /> | 102 <expand macro="citations"/> |
| 87 </tool> | 103 </tool> |
| 88 | 104 |