# HG changeset patch
# User rdvelazquez
# Date 1524163179 14400
# Node ID 9dc36a1975e83b1f1d100645c357b3c3e12cde19
# Parent  d975f8166fc86e3f5f14f74e420a282eaf0096d5
planemo upload for repository https://github.com/veg/hivclustering/ commit b'a6d09759f16c40d4607d30f4bb28772e74c07021\n'-dirty

diff -r d975f8166fc8 -r 9dc36a1975e8 hivclustering.xml
--- a/hivclustering.xml	Mon Mar 05 10:57:10 2018 -0500
+++ b/hivclustering.xml	Thu Apr 19 14:39:39 2018 -0400
@@ -1,111 +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="hmmer3" multiple="True" label="Input multi-sequence alignment" />
-            </when>
-            <when value="remove">
-                <param argument="--sequences" type="data" format="hmmer3" 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="json" />
-    </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="output" ftype="json" file="hivclustering-out1.json" />
-        </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="output" ftype="json" file="hivclustering-out2.json" />
-        </test>
-    </tests>
-    <help>A Python 3 library that makes inferences on HIV-1 transmission networks.</help>
-</tool>
-
+<?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 d975f8166fc8 -r 9dc36a1975e8 macros.xml
--- a/macros.xml	Mon Mar 05 10:57:10 2018 -0500
+++ b/macros.xml	Thu Apr 19 14:39:39 2018 -0400
@@ -1,9 +1,21 @@
-<?xml version="1.0"?>
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@VERSION@">python-hivclustering</requirement>
-        </requirements>
-    </xml>
-    <token name="@VERSION@">1.3.0</token>
-</macros>
\ No newline at end of file
+<?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 d975f8166fc8 -r 9dc36a1975e8 test-data/hivclustering-in1.csv
--- a/test-data/hivclustering-in1.csv	Mon Mar 05 10:57:10 2018 -0500
+++ b/test-data/hivclustering-in1.csv	Thu Apr 19 14:39:39 2018 -0400
@@ -1,8 +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
+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 d975f8166fc8 -r 9dc36a1975e8 test-data/hivclustering-in2.csv
--- a/test-data/hivclustering-in2.csv	Mon Mar 05 10:57:10 2018 -0500
+++ b/test-data/hivclustering-in2.csv	Thu Apr 19 14:39:39 2018 -0400
@@ -1,29 +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
+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 d975f8166fc8 -r 9dc36a1975e8 test-data/hivclustering-out1.json
--- a/test-data/hivclustering-out1.json	Mon Mar 05 10:57:10 2018 -0500
+++ b/test-data/hivclustering-out1.json	Thu Apr 19 14:39:39 2018 -0400
@@ -1,206 +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
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+}
diff -r d975f8166fc8 -r 9dc36a1975e8 test-data/hivclustering-out2.json
--- a/test-data/hivclustering-out2.json	Mon Mar 05 10:57:10 2018 -0500
+++ b/test-data/hivclustering-out2.json	Thu Apr 19 14:39:39 2018 -0400
@@ -1,527 +1,527 @@
-{
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