diff stacks_pstacks.xml @ 3:fede8a808d36 draft

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

--- a/stacks_pstacks.xml	Wed Jun 15 06:23:05 2016 -0400
+++ b/stacks_pstacks.xml	Sat Jun 25 17:27:31 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.2">
     <description>find stacks from short reads mapped to a reference genome</description>
     <macros>
         <import>macros.xml</import>
@@ -14,12 +14,12 @@
         &&
 
         #if $sample.ext == "sam":
-            #set $data_path = splitext($sample.name)[0]
+            #set $data_path = splitext($sample.element_identifier)[0]
             #set $data_path = re.sub(r'\.1$', '', $data_path)
             #set $data_path = "stacks_inputs/" + $data_path + ".sam"
             #set inputype = "sam"
         #else:
-            #set $data_path = splitext($sample.name)[0]
+            #set $data_path = splitext($sample.element_identifier)[0]
             #set $data_path = re.sub(r'\.1$', '', $data_path)
             #set $data_path = "stacks_inputs/" + $data_path + ".bam"
             #set inputype = "bam"
@@ -58,8 +58,10 @@
 
             -o stacks_outputs
 
+             > pstacks.log 2>&1
+
             ## If input is in bam format, stacks will output gzipped files (no option to control this)
-            && gunzip stacks_outputs/*.gz
+            && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
     ]]></command>
 
     <inputs>
@@ -77,11 +79,13 @@
     </inputs>
 
     <outputs>
+        <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
+
         <collection name="tabs" type="list" label="Stacks from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />>
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />>
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
     </outputs>
 
@@ -90,6 +94,12 @@
             <param name="sample" value="refmap/PopA_01.bam" ftype="bam" />
             <param name="sample_id" value="4" />
 
+            <output name="output_log">
+                <assert_contents>
+                    <has_text text="done." />
+                </assert_contents>
+            </output>
+
             <output_collection name="tabs">
                 <element name="PopA_01.tags">
                     <assert_contents>