Mercurial > repos > iuc > ivar_variants
comparison ivar_variants.xml @ 15:045d6d00f606 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
| author | iuc |
|---|---|
| date | Tue, 27 Jun 2023 17:13:41 +0000 |
| parents | ed28dd32141c |
| children |
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| 14:230b05597996 | 15:045d6d00f606 |
|---|---|
| 1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
| 2 <description>Call variants from aligned BAM file</description> | 2 <description>Call variants from aligned BAM file</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"/> |
| 57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> | 57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> |
| 58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> | 58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> |
| 59 </data> | 59 </data> |
| 60 </outputs> | 60 </outputs> |
| 61 <tests> | 61 <tests> |
| 62 <test expect_num_outputs="1"> | 62 <test expect_num_outputs="1"> <!-- test 1 --> |
| 63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> | 63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
| 64 <param name="ref" value="zika/db/PRV.fa"/> | 64 <param name="ref" value="zika/db/PRV.fa"/> |
| 65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/> | 65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/> |
| 66 </test> | 66 </test> |
| 67 <test expect_num_outputs="1"> | 67 <test expect_num_outputs="1"> <!-- test 2 --> |
| 68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> | 68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
| 69 <param name="ref" value="zika/db/PRV.fa"/> | 69 <param name="ref" value="zika/db/PRV.fa"/> |
| 70 <conditional name="output_format"> | 70 <conditional name="output_format"> |
| 71 <param name="choice" value="vcf"/> | 71 <param name="choice" value="vcf"/> |
| 72 </conditional> | 72 </conditional> |
| 73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/> | 73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/> |
| 74 </test> | 74 </test> |
| 75 <test expect_num_outputs="2"> | 75 <test expect_num_outputs="2"> <!-- test 3 --> |
| 76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> | 76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
| 77 <param name="ref" value="zika/db/PRV.fa"/> | 77 <param name="ref" value="zika/db/PRV.fa"/> |
| 78 <conditional name="output_format"> | 78 <conditional name="output_format"> |
| 79 <param name="choice" value="tabular_and_vcf"/> | 79 <param name="choice" value="tabular_and_vcf"/> |
| 80 <param name="pass_only" value="true"/> | 80 <param name="pass_only" value="true"/> |
| 81 </conditional> | 81 </conditional> |
| 82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/> | 82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/> |
| 83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> | 83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> |
| 84 </test> | 84 </test> |
| 85 <test expect_num_outputs="1"> | 85 <test expect_num_outputs="1"> <!-- test 4 --> |
| 86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> | 86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
| 87 <param name="ref" value="zika/db/PRV.fa"/> | 87 <param name="ref" value="zika/db/PRV.fa"/> |
| 88 <param name="gtf" value="zika/db/PRV.gff"/> | 88 <param name="gtf" value="zika/db/PRV.gff"/> |
| 89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/> | 89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/> |
| 90 </test> | 90 </test> |
| 91 <test expect_num_outputs="2"> | 91 <test expect_num_outputs="2"> <!-- test 5 --> |
| 92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> | 92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
| 93 <param name="ref" value="zika/db/PRV.fa"/> | 93 <param name="ref" value="zika/db/PRV.fa"/> |
| 94 <param name="gtf" value="zika/db/PRV.gff"/> | 94 <param name="gtf" value="zika/db/PRV.gff"/> |
| 95 <conditional name="output_format"> | 95 <conditional name="output_format"> |
| 96 <param name="choice" value="tabular_and_vcf"/> | 96 <param name="choice" value="tabular_and_vcf"/> |