Mercurial > repos > iuc > stacks2_refmap

diff stacks_refmap.xml @ 2:6dafad990086 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:26:37 -0400
parents 319b10947ec1
children 4f65e343ecdf
line wrap: on
line diff
--- a/stacks_refmap.xml	Mon Sep 30 14:15:21 2019 -0400
+++ b/stacks_refmap.xml	Thu Jul 16 07:26:37 2020 -0400
@@ -31,7 +31,7 @@
 
     <inputs>
         <expand macro="bam_input_macro"/>
-        <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"/>
         <param name="paired_select" type="select" label="Paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input">
             <option value="" selected="true">single/paired</option>
             <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
@@ -50,42 +50,40 @@
 
     <tests>
         <!-- bams as list -->
-        <test>
+        <test expect_num_outputs="7">
             <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="add_log" value="yes" />
-            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="add_log" value="yes"/>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2">
-                <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
-                <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
+                <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
+                <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
             </output_collection>
             <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
             <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
             <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/>
             <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/>
             <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/>
-            <output ftype="tabular" name="out_sql" value="refmap/populations.markers.tsv"/>
         </test>
-        <test>
+        <test expect_num_outputs="7">
             <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <param name="paired_select" value="--unpaired"/>
-            <param name="model_options|var_alpha" value="0.1" />
-            <param name="model_options|gt_alpha" value="0.1" />
+            <param name="model_options|var_alpha" value="0.1"/>
+            <param name="model_options|gt_alpha" value="0.1"/>
             <assert_command>
-                <has_text text="--unpaired" />
-                <has_text text="--var-alpha 0.1" />
-                <has_text text="--gt-alpha 0.1" />
+                <has_text text="--unpaired"/>
+                <has_text text="--var-alpha 0.1"/>
+                <has_text text="--gt-alpha 0.1"/>
             </assert_command>
-            <param name="add_log" value="yes" />
-            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
+            <param name="add_log" value="yes"/>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2"/>
             <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
             <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
             <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>
@@ -148,5 +146,5 @@
 @STACKS_INFOS@
 ]]>
     </help>
-    <expand macro="citation" />
+    <expand macro="citation"/>
 </tool>