diff stacks_rxstacks.xml @ 3:55814b6afe69 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

--- a/stacks_rxstacks.xml	Wed Jun 15 06:23:37 2016 -0400
+++ b/stacks_rxstacks.xml	Sat Jun 25 17:27:52 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.1">
     <description>make corrections to genotype and haplotype calls</description>
     <macros>
         <import>macros.xml</import>
@@ -13,10 +13,10 @@
 
         #for $input_file in $input_col:
             #set $ext = ""
-            #if not str($input_file.name).endswith('.tsv'):
+            #if not str($input_file.element_identifier).endswith('.tsv'):
                 #set $ext = ".tsv"
             #end if
-            ln -s "${input_file}" "stacks_inputs/${input_file.name}${ext}" &&
+            ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
         #end for
 
         rxstacks
@@ -95,19 +95,19 @@
         </data>
 
         <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
 
         <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
 
         <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
 
         <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
     </outputs>