# HG changeset patch
# User iuc
# Date 1528974278 14400
# Node ID ef842bb94d1fe3af058bbbdbca49d8c5e232f3ff

planemo upload for repository https://github.com/veg/hivclustering/ commit 7d666f963da2c5e3b17c313526cc6169f3242c3c

diff -r 000000000000 -r ef842bb94d1f hivclustering.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hivclustering.xml	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +1,123 @@
+<?xml version="1.0"?>
+<tool id="hivclustering" name="Make inferences" version="@VERSION@.0">
+    <description>on HIV-1 transmission networks using HIVClustering</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        hivnetworkcsv --input '$input' $cluster $multiple_edges $singletons $centralities
+            --threshold $threshold --exclude $exclude --triangles $triangles --format $format
+            #if $contamination.contaminants != 'ignore':
+                --contaminants $contamination.contaminants
+                --contaminant-file '$contamination.contaminant_file'
+            #end if
+            #if $edges.edge_filtering != 'ignore':
+                --edge-filtering $edges.edge_filtering
+                --sequences '$sequences'
+            #end if
+            #if $uds:
+                --uds '$uds'
+            #end if
+            #if $edi:
+                --edi '$edi'
+            #end if
+            #if $old_edi:
+                --old_edi '$old_edi'
+            #end if
+            #if $resistance:
+                --resistance '$resistance'
+            #end if
+            #if $attributes:
+                --attributes '$attributes'
+            #end if
+            #if $filter:
+                --filter '$filter'
+            #end if
+            --json > hivcluster.json
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links"/>
+        <conditional name="contamination">
+            <param argument="--contaminants" type="select" label="How to treat contamination">
+                <option value="ignore" selected="True">Do nothing</option>
+                <option value="report">Report</option>
+                <option value="remove">Remove</option>
+            </param>
+            <when value="ignore"/>
+            <when value="report">
+                <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
+            </when>
+            <when value="remove">
+                <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
+            </when>
+        </conditional>
+        <conditional name="edges">
+            <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges">
+                <option value="ignore" selected="True">Do not mark</option>
+                <option value="report">For display</option>
+                <option value="remove">For removal</option>
+            </param>
+            <when value="ignore"/>
+            <when value="report">
+                <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
+            </when>
+            <when value="remove">
+                <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
+            </when>
+        </conditional>
+        <param argument="--uds" type="data" format="csv" optional="True" label="Input file with UDS data"/>
+        <param argument="--edi" type="data" format="json" optional="True" label="Input JSON with clinical information"/>
+        <param argument="--old_edi" type="data" format="csv" optional="True" label="Legacy EDI dates in CSV format"/>
+        <param argument="--resistance" type="data" format="csv" optional="True" label="Resistance annotation in JSON format"/>
+        <param argument="--attributes" type="data" format="csv" optional="True" label="Input CSV with node attributes"/>
+        <param argument="--filter" type="data" format="text" optional="True" label="File with IDs to cluster, one per line"/>
+        <param argument="--format" type="select" label="Sequence ID format">
+            <option value="AEH">AEH</option>
+            <option value="LANL">LANL</option>
+            <option value="plain">plain</option>
+        </param>
+        <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence"/>
+        <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"/>
+        <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output"/>
+        <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities"/>
+        <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/>
+        <param argument="--exclude" type="integer" value="1959" label="Only consider sequences isolated after this year"/>
+        <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/>
+    </inputs>
+    <outputs>
+        <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="hivclustering-in1.csv" ftype="csv"/>
+            <param name="format" value="plain"/>
+            <param name="threshold" value="0.8"/>
+            <param name="json" value="True"/>
+            <output name="graph" ftype="hivtrace">
+                <assert_contents>
+                    <has_text text="Cluster sizes"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="hivclustering-in2.csv" ftype="csv"/>
+            <param name="format" value="plain"/>
+            <param name="threshold" value="0.8"/>
+            <param name="json" value="True"/>
+            <output name="graph" ftype="hivtrace">
+                <assert_contents>
+                    <has_text text="Cluster sizes"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+HIVClustering
+-------------
+
+A python library that makes inferences on HIV-1 transmission networks.
+        ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r ef842bb94d1f macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@VERSION@">python-hivclustering</requirement>
+    </requirements>
+  </xml>
+  <token name="@VERSION@">1.3.1</token>
+  <xml name="citations">
+    <citations>
+      <citation type="bibtex">
+                @UNPUBLISHED{spond,
+                    author = "Sergei Kosakovsky Pond",
+                    title = "HyPhy: Hypothesis Testing using Phylogenies",
+                    year = "2000",
+                    note = "http://hyphy.org/",
+                    url = "http://hyphy.org/"}
+            </citation>
+    </citations>
+  </xml>
+</macros>
diff -r 000000000000 -r ef842bb94d1f test-data/hivclustering-in1.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hivclustering-in1.csv	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +1,8 @@
+ID1,ID2,Distance
+B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994
+B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156
+D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974
+B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328
+B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218
+D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246
+B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566
diff -r 000000000000 -r ef842bb94d1f test-data/hivclustering-in2.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hivclustering-in2.csv	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +1,29 @@
+ID1,ID2,Distance
+B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994
+B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856
+B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797
+B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156
+B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328
+B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097
+B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218
+B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044
+B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908
+B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203
+B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566
+B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011
+B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759
+B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206
+B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066
+B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054
+D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586
+B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146
+D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974
+D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948
+B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619
+B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213
+D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626
+B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988
+D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033
+D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088
diff -r 000000000000 -r ef842bb94d1f test-data/hivclustering-out1.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hivclustering-out1.json	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +1,206 @@
+{
+    "Cluster sizes": [
+        4,
+        3
+    ],
+    "Degrees": {
+        "Distribution": [
+            2,
+            3,
+            2
+        ],
+        "Model": "Waring",
+        "fitted": [
+            0.5000721527871422,
+            0.24996196530120798,
+            0.12496295268484243
+        ],
+        "rho": 3287.8967604237114,
+        "rho CI": [
+            698.4419473417928,
+            10000.0
+        ]
+    },
+    "Directed Edges": {
+        "Count": 0,
+        "Reasons for unresolved directions": {
+            "Missing dates": 7
+        }
+    },
+    "Edges": [
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.045156,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "B_US_83_RF_ACC_M17451"
+            ],
+            "source": 2,
+            "support": 0.0,
+            "target": 3
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0296218,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "B_US_86_JRFL_ACC_U63632"
+            ],
+            "source": 2,
+            "support": 0.0,
+            "target": 0
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0327566,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "B_US_90_WEAU160_ACC_U21135"
+            ],
+            "source": 2,
+            "support": 0.0,
+            "target": 1
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.048328,
+            "removed": false,
+            "sequences": [
+                "B_US_83_RF_ACC_M17451",
+                "B_US_86_JRFL_ACC_U63632"
+            ],
+            "source": 3,
+            "support": 0.0,
+            "target": 0
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0408994,
+            "removed": false,
+            "sequences": [
+                "B_US_86_JRFL_ACC_U63632",
+                "B_US_90_WEAU160_ACC_U21135"
+            ],
+            "source": 0,
+            "support": 0.0,
+            "target": 1
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0287246,
+            "removed": false,
+            "sequences": [
+                "D_CD_83_ELI_ACC_K03454_7",
+                "D_CD_83_NDK_ACC_M27323"
+            ],
+            "source": 6,
+            "support": 0.0,
+            "target": 4
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0491974,
+            "removed": false,
+            "sequences": [
+                "D_CD_83_NDK_ACC_M27323",
+                "D_CD_84_84ZR085_ACC_U88822"
+            ],
+            "source": 4,
+            "support": 0.0,
+            "target": 5
+        }
+    ],
+    "HIV Stages": {
+        "Unknown": 7
+    },
+    "Multiple sequences": {
+        "Followup, days": null,
+        "Subjects with": 0
+    },
+    "Network Summary": {
+        "Clusters": 2,
+        "Edges": 7,
+        "Nodes": 7,
+        "Sequences used to make links": 7
+    },
+    "Nodes": [
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 1,
+            "edi": null,
+            "id": "B_FR_83_HXB2_ACC_K03455_5"
+        },
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 1,
+            "edi": null,
+            "id": "B_US_83_RF_ACC_M17451"
+        },
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 1,
+            "edi": null,
+            "id": "B_US_86_JRFL_ACC_U63632"
+        },
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 1,
+            "edi": null,
+            "id": "B_US_90_WEAU160_ACC_U21135"
+        },
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 2,
+            "edi": null,
+            "id": "D_CD_83_ELI_ACC_K03454_7"
+        },
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 2,
+            "edi": null,
+            "id": "D_CD_83_NDK_ACC_M27323"
+        },
+        {
+            "attributes": [],
+            "baseline": null,
+            "cluster": 2,
+            "edi": null,
+            "id": "D_CD_84_84ZR085_ACC_U88822"
+        }
+    ],
+    "Settings": {
+        "contaminants": null,
+        "edge-filtering": null,
+        "threshold": 0.8
+    }
+}
diff -r 000000000000 -r ef842bb94d1f test-data/hivclustering-out2.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hivclustering-out2.json	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +1,527 @@
+{
+    "Cluster sizes": [
+        8
+    ],
+    "Degrees": {
+        "Distribution": [
+            0,
+            0,
+            0,
+            0,
+            0,
+            0,
+            8
+        ],
+        "Model": "Negative Binomial",
+        "fitted": null,
+        "rho": 0.0,
+        "rho CI": [
+            0.0,
+            0.0
+        ]
+    },
+    "Directed Edges": {
+        "Count": 0,
+        "Reasons for unresolved directions": {
+            "Missing dates": 28
+        }
+    },
+    "Edges": [
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.045156,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "B_US_83_RF_ACC_M17451"
+            ],
+            "source": 3,
+            "support": 0.0,
+            "target": 4
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0296218,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "B_US_86_JRFL_ACC_U63632"
+            ],
+            "source": 3,
+            "support": 0.0,
+            "target": 0
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0327566,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "B_US_90_WEAU160_ACC_U21135"
+            ],
+            "source": 3,
+            "support": 0.0,
+            "target": 1
+        },
+        {
+            "attributes": [
+                "BULK"
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+            "directed": false,
+            "length": 0.0669206,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "D_CD_83_ELI_ACC_K03454_7"
+            ],
+            "source": 3,
+            "support": 0.0,
+            "target": 2
+        },
+        {
+            "attributes": [
+                "BULK"
+            ],
+            "directed": false,
+            "length": 0.0592586,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "D_CD_83_NDK_ACC_M27323"
+            ],
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+            "support": 0.0,
+            "target": 5
+        },
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+                "BULK"
+            ],
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+            "length": 0.0663619,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "D_CD_84_84ZR085_ACC_U88822"
+            ],
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+            "target": 6
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+                "BULK"
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+            "length": 0.0847988,
+            "removed": false,
+            "sequences": [
+                "B_FR_83_HXB2_ACC_K03455_5",
+                "D_UG_94_94UG114_ACC_U88824"
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+                "B_US_83_RF_ACC_M17451",
+                "B_US_86_JRFL_ACC_U63632"
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+                "B_US_83_RF_ACC_M17451",
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+            ],
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+            "removed": false,
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+                "B_US_83_RF_ACC_M17451",
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+            ],
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+                "B_US_83_RF_ACC_M17451",
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