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comparison hivclustering.xml @ 1:a175c35ccdce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ commit fb9914c1e5dc3555b3d57926259d76dd9a624039
author iuc
date Sat, 05 Oct 2024 16:40:47 +0000
parents ef842bb94d1f
children a30209d11e12
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0:ef842bb94d1f 1:a175c35ccdce
1 <?xml version="1.0"?> 1 <tool id="hivclustering" name="Make inferences" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="@PROFILE@">
2 <tool id="hivclustering" name="Make inferences" version="@VERSION@.0">
3 <description>on HIV-1 transmission networks using HIVClustering</description> 2 <description>on HIV-1 transmission networks using HIVClustering</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements"/> 6 <expand macro="requirements"/>
45 <option value="report">Report</option> 44 <option value="report">Report</option>
46 <option value="remove">Remove</option> 45 <option value="remove">Remove</option>
47 </param> 46 </param>
48 <when value="ignore"/> 47 <when value="ignore"/>
49 <when value="report"> 48 <when value="report">
50 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/> 49 <param argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
51 </when> 50 </when>
52 <when value="remove"> 51 <when value="remove">
53 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/> 52 <param argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
54 </when> 53 </when>
55 </conditional> 54 </conditional>
56 <conditional name="edges"> 55 <conditional name="edges">
57 <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges"> 56 <param argument="--edge-filtering" type="select" label="Compute edge support and mark edges">
58 <option value="ignore" selected="True">Do not mark</option> 57 <option value="ignore" selected="True">Do not mark</option>
59 <option value="report">For display</option> 58 <option value="report">For display</option>
60 <option value="remove">For removal</option> 59 <option value="remove">For removal</option>
61 </param> 60 </param>
62 <when value="ignore"/> 61 <when value="ignore"/>
77 <option value="AEH">AEH</option> 76 <option value="AEH">AEH</option>
78 <option value="LANL">LANL</option> 77 <option value="LANL">LANL</option>
79 <option value="plain">plain</option> 78 <option value="plain">plain</option>
80 </param> 79 </param>
81 <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence"/> 80 <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence"/>
82 <param name="multiple_edges" argument="--multiple-edges" type="boolean" truevalue="--multiple-edges" falsevalue="" label="Permit multiple edges to link the same pair of nodes in the network"/> 81 <param argument="--multiple-edges" type="boolean" truevalue="--multiple-edges" falsevalue="" label="Permit multiple edges to link the same pair of nodes in the network"/>
83 <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output"/> 82 <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output"/>
84 <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities"/> 83 <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities"/>
85 <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/> 84 <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/>
86 <param argument="--exclude" type="integer" value="1959" label="Only consider sequences isolated after this year"/> 85 <param argument="--exclude" type="integer" value="1959" label="Only consider sequences isolated after this year"/>
87 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/> 86 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/>
92 <tests> 91 <tests>
93 <test> 92 <test>
94 <param name="input" value="hivclustering-in1.csv" ftype="csv"/> 93 <param name="input" value="hivclustering-in1.csv" ftype="csv"/>
95 <param name="format" value="plain"/> 94 <param name="format" value="plain"/>
96 <param name="threshold" value="0.8"/> 95 <param name="threshold" value="0.8"/>
97 <param name="json" value="True"/>
98 <output name="graph" ftype="hivtrace"> 96 <output name="graph" ftype="hivtrace">
99 <assert_contents> 97 <assert_contents>
100 <has_text text="Cluster sizes"/> 98 <has_text text="Cluster sizes"/>
101 </assert_contents> 99 </assert_contents>
102 </output> 100 </output>
103 </test> 101 </test>
104 <test> 102 <test>
105 <param name="input" value="hivclustering-in2.csv" ftype="csv"/> 103 <param name="input" value="hivclustering-in2.csv" ftype="csv"/>
106 <param name="format" value="plain"/> 104 <param name="format" value="plain"/>
107 <param name="threshold" value="0.8"/> 105 <param name="threshold" value="0.8"/>
108 <param name="json" value="True"/>
109 <output name="graph" ftype="hivtrace"> 106 <output name="graph" ftype="hivtrace">
110 <assert_contents> 107 <assert_contents>
111 <has_text text="Cluster sizes"/> 108 <has_text text="Cluster sizes"/>
112 </assert_contents> 109 </assert_contents>
113 </output> 110 </output>