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comparison hivclustering.xml @ 2:9dc36a1975e8 draft

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planemo upload for repository https://github.com/veg/hivclustering/ commit b'a6d09759f16c40d4607d30f4bb28772e74c07021\n'-dirty
author rdvelazquez
date Thu, 19 Apr 2018 14:39:39 -0400
parents d975f8166fc8
children 8a6f3d2a2d23
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1:d975f8166fc8 2:9dc36a1975e8
2 <tool id="hivclustering" name="Make inferences" version="@VERSION@.0"> 2 <tool id="hivclustering" name="Make inferences" version="@VERSION@.0">
3 <description>on HIV-1 transmission networks using HIVClustering</description> 3 <description>on HIV-1 transmission networks using HIVClustering</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[ 9 hivnetworkcsv --input $input $cluster $multiple_edges $singletons $centralities
10 hivnetworkcsv --input $input $cluster $multiple_edges $singletons $centralities 10 --threshold $threshold --exclude $exclude --triangles $triangles --format $format
11 --threshold $threshold --exclude $exclude --triangles $triangles --format $format 11 #if $contamination.contaminants != 'ignore':
12 #if $contamination.contaminants != 'ignore': 12 --contaminants $contamination.contaminants
13 --contaminants $contamination.contaminants 13 --contaminant-file '$contamination.contaminant_file'
14 --contaminant-file $contamination.contaminant_file 14 #end if
15 #end if 15 #if $edges.edge_filtering != 'ignore':
16 #if $edges.edge_filtering != 'ignore': 16 --edge-filtering $edges.edge_filtering
17 --edge-filtering $edges.edge_filtering 17 --sequences $sequences
18 --sequences $sequences 18 #end if
19 #end if 19 #if $uds:
20 #if $uds: 20 --uds $uds
21 --uds $uds 21 #end if
22 #end if 22 #if $edi:
23 #if $edi: 23 --edi $edi
24 --edi $edi 24 #end if
25 #end if 25 #if $old_edi:
26 #if $old_edi: 26 --old_edi $old_edi
27 --old_edi $old_edi 27 #end if
28 #end if 28 #if $resistance:
29 #if $resistance: 29 --resistance $resistance
30 --resistance $resistance 30 #end if
31 #end if 31 #if $attributes:
32 #if $attributes: 32 --attributes $attributes
33 --attributes $attributes 33 #end if
34 #end if 34 #if $filter:
35 #if $filter: 35 --filter '$filter'
36 --filter $filter 36 #end if
37 #end if 37 --json > hivcluster.json
38 --json > hivcluster.json 38 ]]>
39 ]]>
40 </command> 39 </command>
41 <inputs> 40 <inputs>
42 <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links" /> 41 <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links"/>
43 <conditional name="contamination"> 42 <conditional name="contamination">
44 <param argument="--contaminants" type="select" label="How to treat contamination"> 43 <param argument="--contaminants" type="select" label="How to treat contamination">
45 <option value="ignore" selected="True">Do nothing</option> 44 <option value="ignore" selected="True">Do nothing</option>
46 <option value="report">Report</option> 45 <option value="report">Report</option>
47 <option value="remove">Remove</option> 46 <option value="remove">Remove</option>
48 </param> 47 </param>
49 <when value="ignore" /> 48 <when value="ignore"/>
50 <when value="report"> 49 <when value="report">
51 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs" /> 50 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
52 </when> 51 </when>
53 <when value="remove"> 52 <when value="remove">
54 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs" /> 53 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
55 </when> 54 </when>
56 </conditional> 55 </conditional>
57 <conditional name="edges"> 56 <conditional name="edges">
58 <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges"> 57 <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> 58 <option value="ignore" selected="True">Do not mark</option>
60 <option value="report">For display</option> 59 <option value="report">For display</option>
61 <option value="remove">For removal</option> 60 <option value="remove">For removal</option>
62 </param> 61 </param>
63 <when value="ignore" /> 62 <when value="ignore"/>
64 <when value="report"> 63 <when value="report">
65 <param argument="--sequences" type="data" format="hmmer3" multiple="True" label="Input multi-sequence alignment" /> 64 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
66 </when> 65 </when>
67 <when value="remove"> 66 <when value="remove">
68 <param argument="--sequences" type="data" format="hmmer3" multiple="True" label="Input multi-sequence alignment" /> 67 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
69 </when> 68 </when>
70 </conditional> 69 </conditional>
71 <param argument="--uds" type="data" format="csv" optional="True" label="Input file with UDS data" /> 70 <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" /> 71 <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" /> 72 <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" /> 73 <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" /> 74 <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" /> 75 <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"> 76 <param argument="--format" type="select" label="Sequence ID format">
78 <option value="AEH">AEH</option> 77 <option value="AEH">AEH</option>
79 <option value="LANL">LANL</option> 78 <option value="LANL">LANL</option>
80 <option value="plain">plain</option> 79 <option value="plain">plain</option>
81 </param> 80 </param>
82 <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence" /> 81 <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" /> 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"/>
84 <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output" /> 83 <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" /> 84 <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" /> 85 <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" /> 86 <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" /> 87 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/>
89 </inputs> 88 </inputs>
90 <outputs> 89 <outputs>
91 <data name="graph" from_work_dir="hivcluster.json" format="json" /> 90 <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/>
92 </outputs> 91 </outputs>
93 <tests> 92 <tests>
94 <test> 93 <test>
95 <param name="input" value="hivclustering-in1.csv" ftype="csv" /> 94 <param name="input" value="hivclustering-in1.csv" ftype="csv"/>
96 <param name="format" value="plain" /> 95 <param name="format" value="plain"/>
97 <param name="threshold" value="0.8" /> 96 <param name="threshold" value="0.8"/>
98 <param name="json" value="True" /> 97 <param name="json" value="True"/>
99 <output name="output" ftype="json" file="hivclustering-out1.json" /> 98 <output name="graph" ftype="hivtrace">
99 <assert_contents>
100 <has_text text="Cluster sizes"/>
101 </assert_contents>
102 </output>
100 </test> 103 </test>
101 <test> 104 <test>
102 <param name="input" value="hivclustering-in2.csv" ftype="csv" /> 105 <param name="input" value="hivclustering-in2.csv" ftype="csv"/>
103 <param name="format" value="plain" /> 106 <param name="format" value="plain"/>
104 <param name="threshold" value="0.8" /> 107 <param name="threshold" value="0.8"/>
105 <param name="json" value="True" /> 108 <param name="json" value="True"/>
106 <output name="output" ftype="json" file="hivclustering-out2.json" /> 109 <output name="graph" ftype="hivtrace">
110 <assert_contents>
111 <has_text text="Cluster sizes"/>
112 </assert_contents>
113 </output>
107 </test> 114 </test>
108 </tests> 115 </tests>
109 <help>A Python 3 library that makes inferences on HIV-1 transmission networks.</help> 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"/>
110 </tool> 123 </tool>
111