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comparison virAnnot_otu.xml @ 2:96aafcc372f7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
author iuc
date Tue, 13 May 2025 11:51:51 +0000
parents 7e160902125e
children
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1:7e160902125e 2:96aafcc372f7
1 <tool id="virannot_otu" name="virAnnot OTU" version="1.1.0+galaxy0" profile="21.05"> 1 <tool id="virannot_otu" name="virAnnot OTU" version="@TOOL_VERSION@+galaxy0" profile="21.05">
2 <description>create viral OTUs based on RPS and Blast annotations</description> 2 <description>create viral OTUs based on RPS and Blast annotations</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
39 #end for 39 #end for
40 -p '$percentage' 40 -p '$percentage'
41 -vp '$viral_portion' 41 -vp '$viral_portion'
42 -mpl '$min_prot_length' 42 -mpl '$min_prot_length'
43 -tp '$__tool_directory__/' 43 -tp '$__tool_directory__/'
44 -m '$merge_rdrp'
44 -o otu_output 45 -o otu_output
45 46
46 && zip -r out.zip otu_output 47 && zip -r out.zip otu_output
47 48
48 ]]></command> 49 ]]></command>
64 <option value="80">80</option> 65 <option value="80">80</option>
65 <option value="100" selected="true">100</option> 66 <option value="100" selected="true">100</option>
66 <option value="150">150</option> 67 <option value="150">150</option>
67 <option value="200">200</option> 68 <option value="200">200</option>
68 </param> 69 </param>
70 <param type="select" name="merge_rdrp" label="Do you want to create a merge of RdRp domain ?">
71 <option value="yes">Yes</option>
72 <option value="no" selected="true">No</option>
73 </param>
69 </inputs> 74 </inputs>
70 <outputs> 75 <outputs>
71 <data format="xlsx" name="otu_table" label="${tool.name} on ${on_string}: otu_stats" from_work_dir="otu_output/otu_stats.xlsx" /> 76 <data format="xlsx" name="otu_table" label="${tool.name} on ${on_string}: otu_stats" from_work_dir="otu_output/otu_stats.xlsx" />
72 <data format="zip" name="archive_output" label="${tool.name} on ${on_string}: zip of the complete output" from_work_dir="out.zip" /> 77 <data format="zip" name="archive_output" label="${tool.name} on ${on_string}: zip of the complete output" from_work_dir="out.zip" />
73 </outputs> 78 </outputs>
74 <tests> 79 <tests>
75 <test> 80 <test>
76 <param name="blast_files" value="input_otu_blast_s1.tab,input_otu_blast_s2.tab"/> 81 <param name="blast_files" value="input_otu_blast_s1.tab,input_otu_blast_s2.tab"/>
77 <param name="rps_files" value="rps_s1_out.tab,rps_s2_out.tab"/> 82 <param name="rps_files" value="input_otu_rps_s1.tab,input_otu_rps_s2.tab"/>
78 <param name="fasta_files" value="input_otu_s1.fasta,input_otu_s2.fasta"/> 83 <param name="fasta_files" value="input_otu_s1.fasta,input_otu_s2.fasta"/>
79 <param name="percentage" value="90"/> 84 <param name="percentage" value="90"/>
80 <param name="viral_portion" value="0.3"/> 85 <param name="viral_portion" value="0.3"/>
81 <param name="min_prot_length" value="100"/> 86 <param name="min_prot_length" value="100"/>
82 <!-- check created zip --> 87 <!-- check created zip -->
83 <output name="archive_output"> 88 <output name="archive_output">
84 <assert_contents> 89 <assert_contents>
85 <has_archive_member path=".*\/index.html" /> 90 <has_archive_member path=".*\/index.html" />
86 <has_archive_member path=".*\/pfam00680_RdRP_1/seq_aligned.final_tree.fa" /> 91 <has_archive_member path=".*\/pfam00680_RdRP_1/seq_aligned.final_tree.fa" />
92 </assert_contents>
93 </output>
94 </test>
95 <test>
96 <param name="rps_files" value="input_otu_rps_s1.tab,input_otu_rps_s2.tab"/>
97 <param name="fasta_files" value="input_otu_s1.fasta,input_otu_s2.fasta"/>
98 <param name="percentage" value="90"/>
99 <param name="viral_portion" value="0.3"/>
100 <param name="min_prot_length" value="100"/>
101 <param name="merge_rdrp" value="yes"/>
102 <!-- check created zip -->
103 <output name="archive_output">
104 <assert_contents>
105 <has_archive_member path=".*\/index.html" />
106 <has_archive_member path=".*\/RdRp_merge" />
107 <has_archive_member path=".*\/otu_stats.xlsx" />
87 </assert_contents> 108 </assert_contents>
88 </output> 109 </output>
89 </test> 110 </test>
90 </tests> 111 </tests>
91 <help><![CDATA[ 112 <help><![CDATA[