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comparison hivclustering.xml @ 0:b2bdeb5c06ed draft

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planemo upload for repository https://github.com/veg/hivclustering/ commit b'f8e8fe8f2d8d7dc6ef93a0e72d43ef5f8ad054c5\n'
author veg
date Mon, 05 Mar 2018 10:17:18 -0500
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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">
9 <![CDATA[
10 hivnetworkcsv --input $input $cluster $multiple_edges $singletons $centralities
11 --threshold $threshold --exclude $exclude --triangles $triangles --format $format
12 #if $contamination.contaminants != 'ignore':
13 --contaminants $contamination.contaminants
14 --contaminant-file $contamination.contaminant_file
15 #end if
16 #if $edges.edge_filtering != 'ignore':
17 --edge-filtering $edges.edge_filtering
18 --sequences $sequences
19 #end if
20 #if $uds:
21 --uds $uds
22 #end if
23 #if $edi:
24 --edi $edi
25 #end if
26 #if $old_edi:
27 --old_edi $old_edi
28 #end if
29 #if $resistance:
30 --resistance $resistance
31 #end if
32 #if $attributes:
33 --attributes $attributes
34 #end if
35 #if $filter:
36 --filter $filter
37 #end if
38 --json > hivcluster.json
39 ]]>
40 </command>
41 <inputs>
42 <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links" />
43 <conditional name="contamination">
44 <param argument="--contaminants" type="select" label="How to treat contamination">
45 <option value="ignore" selected="True">Do nothing</option>
46 <option value="report">Report</option>
47 <option value="remove">Remove</option>
48 </param>
49 <when value="ignore" />
50 <when value="report">
51 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs" />
52 </when>
53 <when value="remove">
54 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs" />
55 </when>
56 </conditional>
57 <conditional name="edges">
58 <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges">
59 <option value="ignore" selected="True">Do not mark</option>
60 <option value="report">For display</option>
61 <option value="remove">For removal</option>
62 </param>
63 <when value="ignore" />
64 <when value="report">
65 <param argument="--sequences" type="data" format="hmmer3" multiple="True" label="Input multi-sequence alignment" />
66 </when>
67 <when value="remove">
68 <param argument="--sequences" type="data" format="hmmer3" multiple="True" label="Input multi-sequence alignment" />
69 </when>
70 </conditional>
71 <param argument="--uds" type="data" format="csv" optional="True" label="Input file with UDS data" />
72 <param argument="--edi" type="data" format="json" optional="True" label="Input JSON with clinical information" />
73 <param argument="--old_edi" type="data" format="csv" optional="True" label="Legacy EDI dates in CSV format" />
74 <param argument="--resistance" type="data" format="csv" optional="True" label="Resistance annotation in JSON format" />
75 <param argument="--attributes" type="data" format="csv" optional="True" label="Input CSV with node attributes" />
76 <param argument="--filter" type="data" format="text" optional="True" label="File with IDs to cluster, one per line" />
77 <param argument="--format" type="select" label="Sequence ID format">
78 <option value="AEH">AEH</option>
79 <option value="LANL">LANL</option>
80 <option value="plain">plain</option>
81 </param>
82 <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence" />
83 <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" />
84 <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output" />
85 <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities" />
86 <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold" />
87 <param argument="--exclude" type="integer" value="1959" label="Only consider sequences isolated after this year" />
88 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass" />
89 </inputs>
90 <outputs>
91 <data name="graph" from_work_dir="hivcluster.json" format="json" />
92 </outputs>
93 <tests>
94 <test>
95 <param name="input" value="hivclustering-in1.csv" ftype="csv" />
96 <param name="format" value="plain" />
97 <param name="threshold" value="0.8" />
98 <param name="json" value="True" />
99 <output name="output" ftype="json" file="hivclustering-out1.json" />
100 </test>
101 <test>
102 <param name="input" value="hivclustering-in2.csv" ftype="csv" />
103 <param name="format" value="plain" />
104 <param name="threshold" value="0.8" />
105 <param name="json" value="True" />
106 <output name="output" ftype="json" file="hivclustering-out2.json" />
107 </test>
108 </tests>
109 <help>A Python 3 library that makes inferences on HIV-1 transmission networks.</help>
110 </tool>
111