diff stacks_ustacks.xml @ 4:ff04b3748654 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f

--- a/stacks_ustacks.xml	Sat Jun 25 17:28:03 2016 -0400
+++ b/stacks_ustacks.xml	Mon Sep 26 11:45:47 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.1">
+<tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0">
     <description>align short reads into stacks</description>
     <macros>
         <import>macros.xml</import>
@@ -38,7 +38,7 @@
             -t $inputype
 
             ## Batch description
-            -i $sample_id
+            -i 1
 
             -m $m
             -M $M
@@ -81,8 +81,6 @@
     <inputs>
         <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" />
 
-        <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
-
         <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
         <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
         <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
@@ -115,7 +113,7 @@
 
         <collection name="tabs" type="list" label="Stacks from ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
-            <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" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
@@ -124,7 +122,6 @@
     <tests>
         <test>
             <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
-            <param name="sample_id" value="4" />
 
             <output name="output_log">
                 <assert_contents>
@@ -196,4 +193,3 @@
     </help>
     <expand macro="citation" />
 </tool>
-