# HG changeset patch
# User nml
# Date 1655755596 0
# Node ID 18aad692772aec5304294af20e6652e4c9a6c812
# Parent  9def47f3c1e48dc8b7131ec50f69ca8a66ee009a
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e

diff -r 9def47f3c1e4 -r 18aad692772a aacoverage.xml
--- a/aacoverage.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/aacoverage.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,13 +1,15 @@
-<tool id="aacoverage" name="Amino Acid Coverage" version="0.7.0">
+<tool id="aacoverage" name="Amino Acid Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Builds an aa census and returns its coverage</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
 
-        quasitools aacoverage $input_bam $ref_file $input_genes -o output.csv
+        quasitools aacoverage '${input_bam.name}' $ref_file $input_genes -o output.csv
 
     ]]></command>
     <inputs>
@@ -44,14 +46,5 @@
 A file with one entry per line with the AA position and the coverage at the position.
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolsaacoverage,
-			title = {quasitools aacoverage},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a callaavar.xml
--- a/callaavar.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/callaavar.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,12 +1,15 @@
-<tool id="aavariants" name="Amino Acid Variants" version="0.7.0">
+<tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Identifies amino acid mutations</description>
-    <requirements>
-        <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-		quasitools call aavar $input_bam $ref_file $input_genes 
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+		quasitools call aavar '${input_bam.name}' $ref_file $input_genes 
 		
 		#if $var_file:
 			$var_file 
@@ -69,14 +72,5 @@
 
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolscallaavar,
-			title = {quasitools callaavar},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a callcodonvar.xml
--- a/callcodonvar.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/callcodonvar.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,14 +1,17 @@
-<tool id="callcodonvar" name="Codon Variants" version="0.7.0">
+<tool id="callcodonvar" name="Codon Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         cat $input_genes &&
 
-        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools call codonvar $input_bam $ref_file $offset $input_genes
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+        quasitools call codonvar '${input_bam.name}' $ref_file $offset $input_genes
 
 		#if $var_file:
 			$var_file 
@@ -56,14 +59,5 @@
 a synonymous or non-synonymous mutation.
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolscallcodonvar,
-			title = {quasitools callcodonvar},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a callntvar.xml
--- a/callntvar.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/callntvar.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,12 +1,15 @@
-<tool id="callntvar" name="Nucleotide Variants" version="0.7.0">
+<tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Identifies nucleotide variants</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools call ntvar $input_bam $ref_file
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+        quasitools call ntvar '${input_bam.name}' $ref_file
 
         #if $error_rate:
             -e $error_rate
@@ -45,14 +48,5 @@
 Call nucleotide variants for a given BAM file and a supplied reference file.
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolscallntvar,
-			title = {quasitools callntvar},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a complexity_bam.xml
--- a/complexity_bam.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/complexity_bam.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,12 +1,14 @@
-<tool id="complexity_bam" name="Complexity BAM" version="0.7.0">
-    <requirements>
-        <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+<tool id="complexity_bam" name="Complexity BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' &&
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
 
-        quasitools complexity bam '$ref_file' '$input_bam'  $k -f '$filter_size' -o output.csv
+        quasitools complexity bam '$ref_file' '${input_bam.name}'  $k -f '$filter_size' -o output.csv
 
     ]]></command>
     <inputs>
@@ -44,14 +46,5 @@
 
 
 ]]></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>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a complexity_fasta.xml
--- a/complexity_fasta.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/complexity_fasta.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,7 +1,8 @@
-<tool id="complexity_fasta" name="Complexity FASTA" version="0.7.0">    
-    <requirements>
-        <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+<tool id="complexity_fasta" name="Complexity FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         quasitools complexity fasta '$input_fasta' -o output.csv
@@ -38,14 +39,5 @@
 
 
 ]]></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>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a consensus.xml
--- a/consensus.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/consensus.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,12 +1,15 @@
-<tool id="consensus" name="Consensus Sequence" version="0.7.0">
+<tool id="consensus" name="Consensus Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Generate a consensus sequence from a BAM file</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools consensus $input_bam $ref_file
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+        quasitools consensus '${input_bam.name}' $ref_file
 
         #if $fasta_id.type == 'default':
             -i '${input_bam.element_identifier}'
@@ -88,14 +91,5 @@
 When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated.
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolsconsensus,
-			title = {quasitools consensus},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a distance.xml
--- a/distance.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/distance.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,8 +1,9 @@
-<tool id="distance" name="Quasispecies Distance" version="0.7.0">
+<tool id="distance" name="Quasispecies Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Calculate the evolutionary distance between viral quasispecies.</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         #for $bam_file in $bam_files
@@ -114,14 +115,5 @@
 A CSV file containing a matrix of similarities or distances, as requested by the user.
 
     ]]></help>
-    <citations>
-        <citation type="bibtex">
-            @misc{GitHubquasitoolsdistance,
-            title = {quasitools distance},
-            publisher = {phac-nml},
-            journal = {GitHub repository},
-            url = {https://github.com/phac-nml/quasitools},
-            }
-        </citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a dnds.xml
--- a/dnds.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/dnds.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,8 +1,9 @@
-<tool id="dnds" name="dNdS Report" version="0.7.0">
+<tool id="dnds" name="dNdS Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Calculate the dN/dS value for each region in a bed file</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         quasitools dnds $csv_file $ref_file $offset -o output.csv
@@ -36,14 +37,5 @@
 Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants).
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolsdnds,
-			title = {quasitools dnds},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a drmutations.xml
--- a/drmutations.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/drmutations.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,12 +1,15 @@
-<tool id="drmutations" name="Drug Resistance Mutations" version="0.7.0">
+<tool id="drmutations" name="Drug Resistance Mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description></description>
-    <requirements>
-        <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools drmutations $input_bam $ref_file $var_file $input_genes
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+        quasitools drmutations '${input_bam.name}' $ref_file $var_file $input_genes
 
         #if $mutation_db:
           $mutation_db
@@ -81,14 +84,5 @@
 A CSV file containing the drug resistant mutations found.
 
     ]]></help>
-	<citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolsdrmutations,
-			title = {quasitools drmutations},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-			</citation>   
-	</citations>
+	<expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a hydra.xml
--- a/hydra.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/hydra.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,8 +1,9 @@
-<tool id="hydra" name="Hydra pipeline" version="0.5.1">
+<tool id="hydra" name="Hydra pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Identifies drug resistance within an NGS dataset</description>
-    <requirements>
-          <requirement type="package" version="0.5.1">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         quasitools hydra
@@ -181,7 +182,7 @@
         <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
         <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
         <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
-        <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
+        <data format="txt" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.aavf" />
         <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
         <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" >
             <filter>consensus['consensus_bool'] == "true_consensus"</filter>
@@ -221,9 +222,9 @@
             </output>
             <output name="output_aa_mt">
                 <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\s101\sP\sPASS\s0.1423\s1574\sWC=aaa;MC=CCa;MCF=0.1423;CAT=NNRTI;SRVL=Yes" />
-                    <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." />
+                    <has_text_matching expression="#CHROM\tGENE\tPOS\tREF\tALT\tFILTER\tALT_FREQ\tCOVERAGE\tINFO"/>
+                    <has_text_matching expression="hxb2_pol\tRT\t101\tK\tP\tPASS\t0.1423\t1574\tRC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes" />
+                    <has_text_matching expression="hxb2_pol\tRT\t101\tK\tT\tmf0.01\t0.0013\t1574\tRC=aaa;AC=aCa;ACF=0.0013;CAT=.;SRVL=." />
                 </assert_contents>
             </output>
            
@@ -280,7 +281,7 @@
         * dr_report.csv
         * filtered.fastq
         * hydra.vcf
-        * mutation_report.hmcf
+        * mutation_report.aavf
         * stats.txt
 
 The description of each of these directories/files are as follows:
@@ -292,7 +293,7 @@
     * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
     * __filtered.fastq__: The reads remaining after the filtering stage.
     * __hydra.vcf__: The variants found by the pipeline.
-    * __mutation_report.hmcf__: The AA mutations found by the pipeline.
+    * __mutation_report.aavf__: The AA mutations found by the pipeline.
     * __stats.txt__: A log file detailing size after filtering and major stages.
 
 The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below.
@@ -302,30 +303,23 @@
     Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage
     RT,NNRTI,Yes,K,103,N,9.03,155
 
-The __mutation_report.hmcf__ files is our custom VCF like file which details all of the AA mutations found by the pipeline. An example if this file is given below.
+The __mutation_report.aavf__ file is in AAVF format (https://github.com/winhiv/aavf-spec), an amino acid variant format inspired by the VCF format. The __mutation_report.aavf__ file details all of the AA mutations found by the pipeline. An example if this file is given below.
 
-Example: __mutation_report.hmcf__
+Example: __mutation_report.aavf__
 
-    ##fileformat=HMCFv1
-    ##fileDate=20150008
-    ##source=HyDRA
-    ##reference=/home/ericenns/hydra/var/hxb2_pol.fas
-    ##INFO=<ID=MC,Number=.,Description="String">
-    ##INFO=<ID=MCF,Number=.,Description="String">
-    ##INFO=<ID=WC,Number=.,Description="String">
-    ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01">
-    #GENE   CATEGORY        SURVEILLANCE    TYPE    WILDTYPE        POS     MUTANT  FILTER  MUTANT_FREQ     COVERAGE INFO
-    RT      NNRTI   Yes     mutation        K       103     N       PASS    0.0903  155     WC=aaa;MC=aaC;MCF=0.0903
+    ##fileformat=AAVFv1.0
+    ##fileDate=20220615
+    ##source=quasitools:hydra
+    ##reference=hxb2_pol.fas
+    ##INFO=<ID=RC,Number=1,Type=String,Description="Reference Codon">
+    ##INFO=<ID=AC,Number=.,Type=String,Description="Alternate Codon">
+    ##INFO=<ID=ACF,Number=.,Type=Float,Description="Alternate Codon Frequency,for each Alternate Codon,in the same order aslisted.">
+    ##INFO=<ID=CAT,Number=.,Type=String,Description="Drug Resistance Category">
+    ##INFO=<ID=SRVL,Number=.,Type=String,Description="Drug Resistance Surveillance">
+    ##FILTER=<ID=af0.01,Description="Set if True; alt_freq<0.01">
+    #CHROM	GENE	POS	REF	ALT	FILTER	ALT_FREQ	COVERAGE	INFO
+    hxb2_pol	RT	101	K	P	PASS	0.1423	1574	RC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes
 
     ]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolshydra,
-			title = {quasitools hydra},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff -r 9def47f3c1e4 -r 18aad692772a macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">quasitools</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.7.0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{GitHubquasitools,
+                title = {quasitools},
+                publisher = {phac-nml},
+                journal = {GitHub repository},
+                url = {https://github.com/phac-nml/quasitools},
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>
diff -r 9def47f3c1e4 -r 18aad692772a quality.xml
--- a/quality.xml	Tue Aug 06 08:50:28 2019 -0400
+++ b/quality.xml	Mon Jun 20 20:06:36 2022 +0000
@@ -1,8 +1,9 @@
-<tool id="quality" name="Quality control" version="0.7.0">
+<tool id="quality" name="Quality control" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Performs quality control on FASTQ reads.</description>
-    <requirements>
-          <requirement type="package" version="0.7.0">quasitools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         quasitools quality
@@ -167,14 +168,5 @@
 ===============
 
 Perform quality control on FASTQ reads.]]></help>
-    <citations>
-		<citation type="bibtex">
-			@misc{GitHubquasitoolsquality,
-			title = {quasitools quality},
-			publisher = {phac-nml},
-			journal = {GitHub repository},
-			url = {https://github.com/phac-nml/quasitools},
-			}
-		</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>