--- a/stacks_denovomap.xml	Mon Sep 30 14:17:15 2019 -0400
+++ b/stacks_denovomap.xml	Wed Jul 15 17:25:36 2020 -0400
@@ -43,7 +43,7 @@
 
     <inputs>
         <expand macro="fastq_input"/>
-        <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
+        <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/>
         <section name="assembly_options" title="Assembly options" expanded="true">
             <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/>
             <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/>
@@ -52,11 +52,11 @@
             <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
         </section>
 		<section name="pe_options" title="Paired-end options" expanded="true">
-            <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help="" />
+            <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help=""/>
         </section>
 		<section name="popfilter_options" title="Population filtering options" expanded="true">
             <param argument="--min-samples-per-pop" name="min_samples_per_pop" type="integer" value="0" label="minimum percentage of individuals in a population required to process a locus for that population" help="(for populations; default: 0)"/>
-            <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)" />
+            <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)"/>
         </section>
         <expand macro="in_log"/>
     </inputs>
@@ -76,62 +76,63 @@
             used in the pipeline have also a test (should be the first) that test for
             equality thereby it is "ensured" that the pipeline w defaults is doing the same
             as the components w defaults. -->
-        <test>
+        <test expect_num_outputs="11">
             <param name="input_type|input_type_select" value="paired"/>
             <param name="input_type|fqinputs">
                 <collection type="list:paired">
                     <element name="PopA_01">
                         <collection type="paired">
-                            <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
+                            <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
                             <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
                         </collection>
                     </element>
                     <element name="PopA_02">
                         <collection type="paired">
-                            <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
+                            <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
                             <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
                         </collection>
                     </element>
                 </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
             <output_collection name="tabs" count="6">
-                <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="2"/>
+                <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="4"/>
             </output_collection>
             <output_collection name="catalog" type="list" count="3">
-                <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
-                <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
+                <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/>
             </output_collection>
             <output_collection name="matches" type="list" count="2">
-                <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="2"/>
-                <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="2"/>
+                <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/>
             </output_collection>
             <output_collection name="bams" type="list" count="2">
-                <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam" compare="sim_size"/>
-                <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size"  />
+                <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
+                <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
             </output_collection>
             <output_collection name="gstacks_out" type="list" count="2">
-                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
-                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
+                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
+                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
             </output_collection>
             <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
-            <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="sim_size"/>
-            <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" compare="sim_size"/>
+            <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="sim_size" delta_frac="0.01"/>
+            <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
             <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
-            <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv" compare="sim_size"/>
-            <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
+            <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
         </test>
         <!-- SE input as multi selection, defaults testing against the output of the pipeline components -->
-        <test>
+        <test expect_num_outputs="11">
             <param name="input_type|input_type_select" value="single"/>
-            <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
             <output_collection name="tabs" count="6"/>
             <output_collection name="catalog" type="list" count="3"/>
             <output_collection name="matches" type="list" count="2"/>
@@ -142,34 +143,34 @@
             <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
         </test>
         <!-- SE input as list, non-defaults, testing only correct size of the collections -->
-        <test>
+        <test expect_num_outputs="11">
             <param name="input_type|input_type_select" value="paired"/>
             <param name="input_type|fqinputs">
                 <collection type="list">
-                    <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
+                    <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
                     <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
                 </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="assembly_options|M" value="3" />
-            <param name="assembly_options|n" value="3" />
-            <param name="model_options|var_alpha" value="0.1" />
-            <param name="model_options|gt_alpha" value="0.1" />
-            <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="assembly_options|M" value="3"/>
+            <param name="assembly_options|n" value="3"/>
+            <param name="model_options|var_alpha" value="0.1"/>
+            <param name="model_options|gt_alpha" value="0.1"/>
+            <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates"/>
             <param name="popfilter_options|min_samples_per_pop" value="1"/>
-            <param name="popfilter_options|min_populations" value="0" />
+            <param name="popfilter_options|min_populations" value="0"/>
             <assert_command>
-                <has_text text="-M 3" />
-                <has_text text="-n 3" />
-                <has_text text="--var-alpha 0.1" />
-                <has_text text="--gt-alpha 0.1" />
-                <has_text text="--rm-pcr-duplicates" />
-                <has_text text="--min-samples-per-pop 1" />
-                <has_text text="--min-populations 0" />
+                <has_text text="-M 3"/>
+                <has_text text="-n 3"/>
+                <has_text text="--var-alpha 0.1"/>
+                <has_text text="--gt-alpha 0.1"/>
+                <has_text text="--rm-pcr-duplicates"/>
+                <has_text text="--min-samples-per-pop 1"/>
+                <has_text text="--min-populations 0"/>
             </assert_command>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
             <output_collection name="tabs" count="6"/>
             <output_collection name="catalog" type="list" count="3"/>
             <output_collection name="matches" type="list" count="2"/>
@@ -180,7 +181,6 @@
             <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
         </test>
     </tests>
 
@@ -244,5 +244,5 @@
 @STACKS_INFOS@
 ]]>
     </help>
-    <expand macro="citation" />
+    <expand macro="citation"/>
 </tool>