# HG changeset patch
# User nml
# Date 1565095828 14400
# Node ID 9def47f3c1e48dc8b7131ec50f69ca8a66ee009a
# Parent  dcd43b402eb3396254c1f7109f2fdd88d1fd94ed
planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35

diff -r dcd43b402eb3 -r 9def47f3c1e4 aacoverage.xml
--- a/aacoverage.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/aacoverage.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="aacoverage" name="Amino Acid Coverage" version="0.4.2">
+<tool id="aacoverage" name="Amino Acid Coverage" version="0.7.0">
     <description>Builds an aa census and returns its coverage</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 callaavar.xml
--- a/callaavar.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/callaavar.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="aavariants" name="Amino Acid Variants" version="0.5.1">
+<tool id="aavariants" name="Amino Acid Variants" version="0.7.0">
     <description>Identifies amino acid mutations</description>
     <requirements>
-        <requirement type="package" version="0.5.1">quasitools</requirement>
+        <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -48,13 +48,13 @@
             <param name="min_freq" value="0.01" />
             <output name="output" >
                 <assert_contents>
-                    <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
-                    <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." />
-                    <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." />
-                    <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." />
-                    <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." />
-                    <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." />
-                    <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." />
+                    <has_text_matching expression="#CHROM"/>
+                    <has_text_matching expression="0.0779" />
+                    <has_text_matching expression="0.0103;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0163;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0148;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0234;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0159;CAT=.;SRVL=." />
                 </assert_contents>
             </output>
         </test>
diff -r dcd43b402eb3 -r 9def47f3c1e4 callcodonvar.xml
--- a/callcodonvar.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/callcodonvar.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="callcodonvar" name="Codon Variants" version="0.5.1">
+<tool id="callcodonvar" name="Codon Variants" version="0.7.0">
     <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 callntvar.xml
--- a/callntvar.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/callntvar.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="callntvar" name="Nucleotide Variants" version="0.5.1">
+<tool id="callntvar" name="Nucleotide Variants" version="0.7.0">
     <description>Identifies nucleotide variants</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 complexity.xml
--- a/complexity.xml	Fri Nov 23 15:43:16 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<tool id="complexity" name="Complexity" version="0.5.1">
-    <description>measures the complexity of the quasispecies reads</description>
-    <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-
-        quasitools complexity $input_fasta > complexity.txt
-
-    ]]></command>
-    <inputs>
-        <param name="input_fasta" type="data" format="fasta" optional="false" label="Aligned FASTA Input" />
-    </inputs>
-    <outputs>
-        <data format="txt" label="Complexity" name="output_complexity" from_work_dir="complexity.txt" />
-    </outputs>
-
-    <tests>
-        <test>
-            <param name="input_fasta" value="msa.fasta" />
-            <output name="output_complexity">
-                <assert_contents>
-                    <has_text text="Number of haplotypes (H) : 8" />
-                    <has_text text="Mutation Frequency (Mfe) : 0.75" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-Quasispecies Complexity
-=======================
-
-Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity.
-
-The measures of complexity are taken from the following work:
-
-Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
-
-
-]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolscomplexity,
-			title = {quasitools complexity},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-	</citations>
-</tool>
diff -r dcd43b402eb3 -r 9def47f3c1e4 complexity_bam.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/complexity_bam.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -0,0 +1,57 @@
+<tool id="complexity_bam" name="Complexity BAM" version="0.7.0">
+    <requirements>
+        <requirement type="package" version="0.7.0">quasitools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+        ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' &&
+
+        quasitools complexity bam '$ref_file' '$input_bam'  $k -f '$filter_size' -o output.csv
+
+    ]]></command>
+    <inputs>
+        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
+        <param name="input_bam" type="data" format="bam" optional="false" label="BAM file" />
+        <param name="k" type="integer" label="k-mer size" value="0" min="0" />
+        <param name="filter_size" type="integer" label="Filter size" value="0" min="0" />
+    </inputs>
+    <outputs>
+        <data format="csv" name="output" from_work_dir="output.csv" />
+    </outputs>
+   <tests>
+        <test>
+            <param name="ref_file" value="generated.fasta" />
+            <param name="input_bam" value="generated.bam" />
+	    <param name="k" value="200" />
+	    <param name="filter_size" value="0" />
+            <output name="output" >
+                <assert_contents>
+                    <has_text text="Position" />
+                    <has_text text="0" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+   
+    <help><![CDATA[
+Quasispecies Complexity
+=======================
+
+Calculates various quasispecies complexity measures on next generation sequenced data from a BAM file and it's corresponding reference file.
+
+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>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscomplexity,
+			title = {quasitools complexity},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
+	</citations>
+</tool>
diff -r dcd43b402eb3 -r 9def47f3c1e4 complexity_fasta.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/complexity_fasta.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -0,0 +1,51 @@
+<tool id="complexity_fasta" name="Complexity FASTA" version="0.7.0">    
+    <requirements>
+        <requirement type="package" version="0.7.0">quasitools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+        quasitools complexity fasta '$input_fasta' -o output.csv
+
+    ]]></command>
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" />  
+    </inputs>
+    <outputs>
+        <data format="csv" name="output" from_work_dir="output.csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fasta" value="msa.fasta" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Number of Haplotypes" />
+		    <has_text text="8" />
+                    <has_text text="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>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscomplexity,
+			title = {quasitools complexity},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
+	</citations>
+</tool>
diff -r dcd43b402eb3 -r 9def47f3c1e4 consensus.xml
--- a/consensus.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/consensus.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="consensus" name="Consensus Sequence" version="0.5.1">
+<tool id="consensus" name="Consensus Sequence" version="0.7.0">
     <description>Generate a consensus sequence from a BAM file</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 distance.xml
--- a/distance.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/distance.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="distance" name="Quasispecies Distance" version="0.5.1">
+<tool id="distance" name="Quasispecies Distance" version="0.7.0">
     <description>Calculate the evolutionary distance between viral quasispecies.</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 dnds.xml
--- a/dnds.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/dnds.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="dnds" name="dNdS Report" version="0.5.1">
+<tool id="dnds" name="dNdS Report" version="0.7.0">
     <description>Calculate the dN/dS value for each region in a bed file</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 drmutations.xml
--- a/drmutations.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/drmutations.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="drmutations" name="Drug Resistance Mutations" version="0.5.1">
+<tool id="drmutations" name="Drug Resistance Mutations" version="0.7.0">
     <description></description>
     <requirements>
-        <requirement type="package" version="0.5.1">quasitools</requirement>
+        <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 hydra.xml
--- a/hydra.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/hydra.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -226,6 +226,7 @@
                     <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." />
                 </assert_contents>
             </output>
+           
             <output name="output_stats">
                 <assert_contents>
                     <has_text text="Input Size: 25000"/>
diff -r dcd43b402eb3 -r 9def47f3c1e4 quality.xml
--- a/quality.xml	Fri Nov 23 15:43:16 2018 -0500
+++ b/quality.xml	Tue Aug 06 08:50:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="quality" name="Quality control" version="0.5.1">
+<tool id="quality" name="Quality control" version="0.7.0">
     <description>Performs quality control on FASTQ reads.</description>
     <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
+          <requirement type="package" version="0.7.0">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
diff -r dcd43b402eb3 -r 9def47f3c1e4 test-data/generated.bai
Binary file test-data/generated.bai has changed
diff -r dcd43b402eb3 -r 9def47f3c1e4 test-data/generated.bam
Binary file test-data/generated.bam has changed
diff -r dcd43b402eb3 -r 9def47f3c1e4 test-data/generated.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generated.fasta	Tue Aug 06 08:50:28 2019 -0400
@@ -0,0 +1,2 @@
+>reference
+AAGAGCGGTGAGGAGTACTCACCTCAATAGACAAGGAGAGCTATATCGCGCAGCATCGCTTCGATATTTTGCTCCTACGCATCCACACGTTGAAAGGGCCAAATGATGGTCGCTCCACTTTCTCTCTAGAACGATCGTTATGTCGAAGTCCAAGCACTACGGGGTACTACAAGTATATTACGAGCCTACTTACCTCCAAA