--- a/hivclustering.xml	Mon Mar 05 10:17:18 2018 -0500
+++ b/hivclustering.xml	Mon Mar 05 10:57:10 2018 -0500
@@ -1,111 +1,111 @@
-<?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="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>
+