Mercurial > repos > rdvelazquez > hivclustering

changeset 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
files hivclustering.xml macros.xml
diffstat 2 files changed, 104 insertions(+), 103 deletions(-) [+]
line wrap: on
line diff
--- a/hivclustering.xml	Thu Apr 19 14:39:39 2018 -0400
+++ b/hivclustering.xml	Mon Mar 25 13:21:35 2019 -0400
@@ -1,12 +1,13 @@
 <?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 $centralities
+  <description>on HIV-1 transmission networks using
+  HIVClustering</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+        hivnetworkcsv --input '$input' $cluster $multiple_edges $singletons $centralities
             --threshold $threshold --exclude $exclude --triangles $triangles --format $format
             #if $contamination.contaminants != 'ignore':
                 --contaminants $contamination.contaminants
@@ -14,110 +15,113 @@
             #end if
             #if $edges.edge_filtering != 'ignore':
                 --edge-filtering $edges.edge_filtering
-                --sequences $sequences
+                --sequences '$sequences'
             #end if
             #if $uds:
-                --uds $uds
+                --uds '$uds'
             #end if
             #if $edi:
-                --edi $edi
+                --edi '$edi'
             #end if
             #if $old_edi:
-                --old_edi $old_edi
+                --old_edi '$old_edi'
             #end if
             #if $resistance:
-                --resistance $resistance
+                --resistance '$resistance'
             #end if
             #if $attributes:
-                --attributes $attributes
+                --attributes '$attributes'
             #end if
             #if $filter:
                 --filter '$filter'
             #end if
+            #if $edge_filter_cycles:
+                --edge-filter-cycles
+            #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[
+        ]]></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 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"/>
+    <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"/>
+  <expand macro="citations"/>
 </tool>
--- a/macros.xml	Thu Apr 19 14:39:39 2018 -0400
+++ b/macros.xml	Mon Mar 25 13:21:35 2019 -0400
@@ -2,20 +2,17 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="@VERSION@">python-hivclustering</requirement>
+      <requirement type="package" version="@VERSION@">
+      python-hivclustering</requirement>
     </requirements>
   </xml>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@VERSION@">1.4.0</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>
+      <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>