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comparison ivar_removereads.xml @ 12:8c05afb547fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author iuc
date Mon, 13 Feb 2023 17:31:02 +0000
parents 7f1cfa4c0e32
children
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11:7f1cfa4c0e32 12:8c05afb547fa
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**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;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**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;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[