diff stacks_ustacks.xml @ 1:21d2aa544835 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"

--- a/stacks_ustacks.xml	Mon Jul 01 10:57:49 2019 -0400
+++ b/stacks_ustacks.xml	Mon Sep 30 14:16:43 2019 -0400
@@ -149,16 +149,16 @@
         <test>
             <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="-m" value="2" />
-            <param name="-M" value="3" />
-            <param name="-N" value="4"/>
-            <param name="-R" value="-R" />
-            <param name="-H" value="-H" />
+            <param name="m" value="2" />
+            <param name="M" value="3" />
+            <param name="N" value="4"/>
+            <param name="R" value="-R" />
+            <param name="H" value="-H" />
             <param name="add_log" value="yes" />
             <assert_command>
                 <has_text text="-m 2" />
                 <has_text text="-M 3" />
-                <has_text text="-N 5" />
+                <has_text text="-N 4" />
                 <has_text text="-R" />
                 <has_text text="-H" />
             </assert_command>
@@ -201,11 +201,11 @@
             <param name="gapped|use_gapped" value="no" />
             <param name="add_log" value="yes" />
             <assert_command>
-                <has_text text="--model_type bounded" />
+                <has_text text="--model_type snp" />
                 <has_text text="--alpha 0.1" />
-                <has_text text="--bound_low 0.1" />
-                <has_text text="--bound_high 0.5" />
-                <has_text text="--bc_err_freq 0.1" />
+                <not_has_text text="--bound_low 0.1" />
+                <not_has_text text="--bound_high 0.5" />
+                <not_has_text text="--bc_err_freq 0.1" />
                 <has_text text="--disable-gapped" />
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
@@ -227,7 +227,7 @@
                     <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
                 </collection>
             </param>
-            <param name="assembly_options|keep_high_cov" value="--keep-high-cov"/>
+            <param name="assembly_options|keep_high_cov" value="true"/>
             <param name="assembly_options|d" value="-d" />
             <param name="assembly_options|high_cov_thres" value="2.0"/>
             <param name="assembly_options|max_locus_stacks" value="4" />
@@ -243,7 +243,7 @@
                 <has_text text="--max_locus_stacks 4" />
                 <has_text text="--k_len 12" />
                 <has_text text="--max_gaps 3" />
-                <has_text text="--min_aln_len 3" />
+                <has_text text="--min_aln_len 0.7" />
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
             <output_collection name="tabs" count="6">