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comparison hivclustering.xml @ 3:8a6f3d2a2d23 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ commit b'd932a0c30a3e50d32d210f7cc1f42d82ded17719\n'-dirty
author rdvelazquez
date Mon, 25 Mar 2019 13:21:35 -0400
parents 9dc36a1975e8
children
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2:9dc36a1975e8 3:8a6f3d2a2d23
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
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
4 <macros> 4 HIVClustering</description>
5 <import>macros.xml</import> 5 <macros>
6 </macros> 6 <import>macros.xml</import>
7 <expand macro="requirements"/> 7 </macros>
8 <command detect_errors="exit_code"><![CDATA[ 8 <expand macro="requirements"/>
9 hivnetworkcsv --input $input $cluster $multiple_edges $singletons $centralities 9 <command detect_errors="exit_code"><![CDATA[
10 hivnetworkcsv --input '$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
38 #if $edge_filter_cycles:
39 --edge-filter-cycles
40 #end if
37 --json > hivcluster.json 41 --json > hivcluster.json
38 ]]> 42 ]]></command>
39 </command> 43 <inputs>
40 <inputs> 44 <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"/> 45 <conditional name="contamination">
42 <conditional name="contamination"> 46 <param argument="--contaminants" type="select" label="How to treat contamination">
43 <param argument="--contaminants" type="select" label="How to treat contamination"> 47 <option value="ignore" selected="True">Do nothing</option>
44 <option value="ignore" selected="True">Do nothing</option> 48 <option value="report">Report</option>
45 <option value="report">Report</option> 49 <option value="remove">Remove</option>
46 <option value="remove">Remove</option> 50 </param>
47 </param> 51 <when value="ignore"/>
48 <when value="ignore"/> 52 <when value="report">
49 <when value="report"> 53 <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"/> 54 </when>
51 </when> 55 <when value="remove">
52 <when value="remove"> 56 <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"/> 57 </when>
54 </when> 58 </conditional>
55 </conditional> 59 <conditional name="edges">
56 <conditional name="edges"> 60 <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"> 61 <option value="ignore" selected="True">Do not mark</option>
58 <option value="ignore" selected="True">Do not mark</option> 62 <option value="report">For display</option>
59 <option value="report">For display</option> 63 <option value="remove">For removal</option>
60 <option value="remove">For removal</option> 64 </param>
61 </param> 65 <when value="ignore"/>
62 <when value="ignore"/> 66 <when value="report">
63 <when value="report"> 67 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
64 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/> 68 </when>
65 </when> 69 <when value="remove">
66 <when value="remove"> 70 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
67 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/> 71 </when>
68 </when> 72 </conditional>
69 </conditional> 73 <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"/> 74 <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"/> 75 <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"/> 76 <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"/> 77 <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"/> 78 <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"/> 79 <param argument="--format" type="select" label="Sequence ID format">
76 <param argument="--format" type="select" label="Sequence ID format"> 80 <option value="AEH">AEH</option>
77 <option value="AEH">AEH</option> 81 <option value="LANL">LANL</option>
78 <option value="LANL">LANL</option> 82 <option value="plain">plain</option>
79 <option value="plain">plain</option> 83 </param>
80 </param> 84 <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"/> 85 <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"/> 86 <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"/> 87 <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"/> 88 <param name="edge_filter_cycles" argument="--edge-filter-cycles" type="boolean" truevalue="--edge-filter-cycles" falsevalue="" label="Filter edges that are in cycles other than triangles"/>
85 <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/> 89 <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"/> 90 <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"/> 91 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/>
88 </inputs> 92 </inputs>
89 <outputs> 93 <outputs>
90 <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/> 94 <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/>
91 </outputs> 95 </outputs>
92 <tests> 96 <tests>
93 <test> 97 <test>
94 <param name="input" value="hivclustering-in1.csv" ftype="csv"/> 98 <param name="input" value="hivclustering-in1.csv" ftype="csv"/>
95 <param name="format" value="plain"/> 99 <param name="format" value="plain"/>
96 <param name="threshold" value="0.8"/> 100 <param name="threshold" value="0.8"/>
97 <param name="json" value="True"/> 101 <param name="json" value="True"/>
98 <output name="graph" ftype="hivtrace"> 102 <output name="graph" ftype="hivtrace">
99 <assert_contents> 103 <assert_contents>
100 <has_text text="Cluster sizes"/> 104 <has_text text="Cluster sizes"/>
101 </assert_contents> 105 </assert_contents>
102 </output> 106 </output>
103 </test> 107 </test>
104 <test> 108 <test>
105 <param name="input" value="hivclustering-in2.csv" ftype="csv"/> 109 <param name="input" value="hivclustering-in2.csv" ftype="csv"/>
106 <param name="format" value="plain"/> 110 <param name="format" value="plain"/>
107 <param name="threshold" value="0.8"/> 111 <param name="threshold" value="0.8"/>
108 <param name="json" value="True"/> 112 <param name="json" value="True"/>
109 <output name="graph" ftype="hivtrace"> 113 <output name="graph" ftype="hivtrace">
110 <assert_contents> 114 <assert_contents>
111 <has_text text="Cluster sizes"/> 115 <has_text text="Cluster sizes"/>
112 </assert_contents> 116 </assert_contents>
113 </output> 117 </output>
114 </test> 118 </test>
115 </tests> 119 </tests>
116 <help><![CDATA[ 120 <help><![CDATA[
117 HIVClustering 121 HIVClustering
118 ------------- 122 -------------
119 123
120 A python library that makes inferences on HIV-1 transmission networks. 124 A python library that makes inferences on HIV-1 transmission networks.
121 ]]></help> 125 ]]></help>
122 <expand macro="citations"/> 126 <expand macro="citations"/>
123 </tool> 127 </tool>