# HG changeset patch
# User nml
# Date 1539350163 14400
# Node ID 9fb9fed714864f6a4dff35025bbc0536e1602124
# Parent  b69e898b8109acb97210d4db849731275525a7e2
planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c

diff -r b69e898b8109 -r 9fb9fed71486 complexity.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/complexity.xml	Fri Oct 12 09:16:03 2018 -0400
@@ -0,0 +1,44 @@
+<tool id="complexity" name="Complexity" version="0.5.0">
+    <description>measures the complexity of the quasispecies reads</description>
+    <requirements>
+          <requirement type="package" version="0.5.0">quasitools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+        quasitools complexity $input_fasta > complexity.txt
+
+    ]]></command>
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta" optional="false" label="Aligned FASTA Input" />
+    </inputs>
+    <outputs>
+        <data format="txt" label="Complexity" name="output_complexity" from_work_dir="complexity.txt" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_fasta" value="msa.fasta" />
+            <output name="output_complexity">
+                <assert_contents>
+                    <has_text text="Number of haplotypes (H) : 8" />
+                    <has_text text="Mutation Frequency (Mfe) : 0.75" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+Quasispecies Complexity
+=======================
+
+Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity.
+
+The measures of complexity are taken from the following work:
+
+Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
+
+
+]]></help>
+    <citations>
+    </citations>
+</tool>
diff -r b69e898b8109 -r 9fb9fed71486 distance.xml
--- a/distance.xml	Fri Aug 24 16:50:28 2018 -0400
+++ b/distance.xml	Fri Oct 12 09:16:03 2018 -0400
@@ -90,28 +90,28 @@
 Quasispecies Distance
 =====================
 
-Determines the evolutionary distance between viral quasispecies.
-Uses the angular cosine distance function by default.
+This tool determines the cosine relatedness between viral quasispecies, reporting either angular cosine distance or cosine similarity as measures of relatedness. These measures of relatedness should be understood as approximations for evolutionary distance and might be useful for performing clustering.
 
 ------
 Inputs
 ------
 
-1. FASTA Consensus file
-2. Two or more BAM files (otherwise tool will throw an error)
+1. A reference FASTA.
+2. At least two BAM files generated in coordination with the above reference.
 
 ----------
 Parameters
 ----------
-1. Normalize pileup (True or False)
+
+1. Normalize pileup (True or False).
 2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference.
-3. Choose how to treat zero coverage regions (keep, remove all, or truncate)
+3. Choose how to treat zero coverage regions (keep, remove all, or truncate).
 
 -------
 Outputs
 -------
 
-CSV containing distance matrix.
+A CSV file containing a matrix of similarities or distances, as requested by the user.
 
     ]]></help>
     <citations>
diff -r b69e898b8109 -r 9fb9fed71486 test-data/msa.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/msa.fasta	Fri Oct 12 09:16:03 2018 -0400
@@ -0,0 +1,16 @@
+>1
+AAA
+>2
+CCC
+>3
+GGG
+>4
+TTT
+>5
+ACG
+>6
+CGT
+>7
+GTA
+>8
+TAC