Mercurial > repos > iuc > hivclustering
comparison hivclustering.xml @ 0:ef842bb94d1f draft default tip
planemo upload for repository https://github.com/veg/hivclustering/ commit 7d666f963da2c5e3b17c313526cc6169f3242c3c
author | iuc |
---|---|
date | Thu, 14 Jun 2018 07:04:38 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:ef842bb94d1f |
---|---|
1 <?xml version="1.0"?> | |
2 <tool id="hivclustering" name="Make inferences" version="@VERSION@.0"> | |
3 <description>on HIV-1 transmission networks using HIVClustering</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 hivnetworkcsv --input '$input' $cluster $multiple_edges $singletons $centralities | |
10 --threshold $threshold --exclude $exclude --triangles $triangles --format $format | |
11 #if $contamination.contaminants != 'ignore': | |
12 --contaminants $contamination.contaminants | |
13 --contaminant-file '$contamination.contaminant_file' | |
14 #end if | |
15 #if $edges.edge_filtering != 'ignore': | |
16 --edge-filtering $edges.edge_filtering | |
17 --sequences '$sequences' | |
18 #end if | |
19 #if $uds: | |
20 --uds '$uds' | |
21 #end if | |
22 #if $edi: | |
23 --edi '$edi' | |
24 #end if | |
25 #if $old_edi: | |
26 --old_edi '$old_edi' | |
27 #end if | |
28 #if $resistance: | |
29 --resistance '$resistance' | |
30 #end if | |
31 #if $attributes: | |
32 --attributes '$attributes' | |
33 #end if | |
34 #if $filter: | |
35 --filter '$filter' | |
36 #end if | |
37 --json > hivcluster.json | |
38 ]]> | |
39 </command> | |
40 <inputs> | |
41 <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links"/> | |
42 <conditional name="contamination"> | |
43 <param argument="--contaminants" type="select" label="How to treat contamination"> | |
44 <option value="ignore" selected="True">Do nothing</option> | |
45 <option value="report">Report</option> | |
46 <option value="remove">Remove</option> | |
47 </param> | |
48 <when value="ignore"/> | |
49 <when value="report"> | |
50 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/> | |
51 </when> | |
52 <when value="remove"> | |
53 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/> | |
54 </when> | |
55 </conditional> | |
56 <conditional name="edges"> | |
57 <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges"> | |
58 <option value="ignore" selected="True">Do not mark</option> | |
59 <option value="report">For display</option> | |
60 <option value="remove">For removal</option> | |
61 </param> | |
62 <when value="ignore"/> | |
63 <when value="report"> | |
64 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/> | |
65 </when> | |
66 <when value="remove"> | |
67 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/> | |
68 </when> | |
69 </conditional> | |
70 <param argument="--uds" type="data" format="csv" optional="True" label="Input file with UDS data"/> | |
71 <param argument="--edi" type="data" format="json" optional="True" label="Input JSON with clinical information"/> | |
72 <param argument="--old_edi" type="data" format="csv" optional="True" label="Legacy EDI dates in CSV format"/> | |
73 <param argument="--resistance" type="data" format="csv" optional="True" label="Resistance annotation in JSON format"/> | |
74 <param argument="--attributes" type="data" format="csv" optional="True" label="Input CSV with node attributes"/> | |
75 <param argument="--filter" type="data" format="text" optional="True" label="File with IDs to cluster, one per line"/> | |
76 <param argument="--format" type="select" label="Sequence ID format"> | |
77 <option value="AEH">AEH</option> | |
78 <option value="LANL">LANL</option> | |
79 <option value="plain">plain</option> | |
80 </param> | |
81 <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"/> | |
83 <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"/> | |
85 <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"/> | |
87 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/> | |
88 </inputs> | |
89 <outputs> | |
90 <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/> | |
91 </outputs> | |
92 <tests> | |
93 <test> | |
94 <param name="input" value="hivclustering-in1.csv" ftype="csv"/> | |
95 <param name="format" value="plain"/> | |
96 <param name="threshold" value="0.8"/> | |
97 <param name="json" value="True"/> | |
98 <output name="graph" ftype="hivtrace"> | |
99 <assert_contents> | |
100 <has_text text="Cluster sizes"/> | |
101 </assert_contents> | |
102 </output> | |
103 </test> | |
104 <test> | |
105 <param name="input" value="hivclustering-in2.csv" ftype="csv"/> | |
106 <param name="format" value="plain"/> | |
107 <param name="threshold" value="0.8"/> | |
108 <param name="json" value="True"/> | |
109 <output name="graph" ftype="hivtrace"> | |
110 <assert_contents> | |
111 <has_text text="Cluster sizes"/> | |
112 </assert_contents> | |
113 </output> | |
114 </test> | |
115 </tests> | |
116 <help><![CDATA[ | |
117 HIVClustering | |
118 ------------- | |
119 | |
120 A python library that makes inferences on HIV-1 transmission networks. | |
121 ]]></help> | |
122 <expand macro="citations"/> | |
123 </tool> |