Mercurial > repos > iuc > ivar_removereads
comparison ivar_removereads.xml @ 12:8c05afb547fa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author | iuc |
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date | Mon, 13 Feb 2023 17:31:02 +0000 |
parents | 7f1cfa4c0e32 |
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11:7f1cfa4c0e32 | 12:8c05afb547fa |
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1 <tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> | 1 <tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
2 <description>Remove reads from trimmed BAM file</description> | 2 <description>Remove reads from trimmed 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"/> |
58 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/> | 58 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/> |
59 <conditional name="amplicons"> | 59 <conditional name="amplicons"> |
60 <param name="computed" value="no"/> | 60 <param name="computed" value="no"/> |
61 <param name="amplicon_info" value="zika/db/pair_information.tsv"/> | 61 <param name="amplicon_info" value="zika/db/pair_information.tsv"/> |
62 </conditional> | 62 </conditional> |
63 <assert_stdout> | |
64 <!-- check that primer pairs are picked up correctly | |
65 from the amplicon info file --> | |
66 <has_text text="400_18_out_L**	400_18_out_R**	400_23_out_L	400_23_out_R	400_32_out_L	400_32_out_R"/> | |
67 </assert_stdout> | |
63 <output name="output_bam" ftype="bam"> | 68 <output name="output_bam" ftype="bam"> |
64 <assert_contents> | 69 <assert_contents> |
65 <has_size value="3185672" delta="1000"/> | 70 <has_size value="3130923" delta="1000"/> |
66 </assert_contents> | 71 </assert_contents> |
67 </output> | 72 </output> |
68 </test> | 73 </test> |
69 <test> | 74 <test> |
70 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/> | 75 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/> |
71 <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/> | 76 <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/> |
72 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/> | 77 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/> |
73 <conditional name="amplicons"> | 78 <conditional name="amplicons"> |
74 <param name="computed" value="yes"/> | 79 <param name="computed" value="yes"/> |
75 </conditional> | 80 </conditional> |
81 <assert_stdout> | |
82 <!-- check that primer pairs are picked up correctly | |
83 from the autogenerated amplicon info file --> | |
84 <has_text text="400_18_out_L**	400_18_out_R**	400_23_out_L	400_23_out_R	400_32_out_L	400_32_out_R"/> | |
85 </assert_stdout> | |
76 <output name="output_bam" ftype="bam"> | 86 <output name="output_bam" ftype="bam"> |
77 <assert_contents> | 87 <assert_contents> |
78 <has_size value="3185672" delta="1000"/> | 88 <has_size value="3130923" delta="1000"/> |
79 </assert_contents> | 89 </assert_contents> |
80 </output> | 90 </output> |
81 </test> | 91 </test> |
82 </tests> | 92 </tests> |
83 <help><![CDATA[ | 93 <help><![CDATA[ |