diff stacks_denovomap.xml @ 1:afdbc7fcce70 draft

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

--- a/stacks_denovomap.xml	Mon Jul 01 11:04:37 2019 -0400
+++ b/stacks_denovomap.xml	Mon Sep 30 14:17:15 2019 -0400
@@ -7,7 +7,11 @@
     <expand macro="version_cmd"/>
     <command detect_errors="aggressive"><![CDATA[
 @FASTQ_INPUT_FUNCTIONS@
-mkdir stacks_inputs stacks_outputs&&
+mkdir stacks_inputs stacks_outputs &&
+
+#if $output_log
+    ln -s '$output_log' stacks_outputs/denovo_map.log &&
+#end if
 
 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" )
 $link_command
@@ -35,7 +39,6 @@
 ## to make it usable in Galaxy (with the downside that we
 ## need to gzip it again for downstream calls like populations)
 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
-&& mv stacks_outputs/denovo_map.log $output_log
     ]]></command>
 
     <inputs>
@@ -161,11 +164,11 @@
             <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="--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_collection name="tabs" count="6"/>
             <output_collection name="catalog" type="list" count="3"/>