changeset 3:10dcc8027778 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

--- a/bamtools-split.xml	Mon Oct 12 11:57:54 2015 -0400
+++ b/bamtools-split.xml	Mon Nov 09 12:04:47 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="bamSplit" name="Split" version="0.0.1" force_history_refresh="True">
+<tool id="bamSplit" name="Split" version="0.0.2" force_history_refresh="True">
   <description>BAM datasets on variety of attributes</description>
   <requirements>
     <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
@@ -6,37 +6,35 @@
   <command>
 
     echo "BAM" > $report &amp;&amp;
-    
+
     #for $bam_count, $input_bam in enumerate( $input_bams ):
-        ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
-        ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
+      ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
+      ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
     #end for
-    
+
     bamtools
     split
-  
+
     #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
-    
+
     ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
 
     #else
-    
+
     ${analysis_type.analysis_type_selector}
-    
+
     #end if
-    
+
     -stub split_bam
-    
+
     #for $bam_count, $input_bam in enumerate( $input_bams ):
         -in "localbam_${bam_count}.bam"
     #end for
-    
+
   </command>
 
   <inputs>
-    <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
-      <param name="input_bam" type="data" format="bam" label="BAM dataset" />
-    </repeat>
+    <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
     <conditional name="analysis_type">
       <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option">
         <option value="-mapped">Mapping status (-mapped)</option>
@@ -52,7 +50,7 @@
       </when>
     </conditional>
   </inputs>
-  
+
   <outputs>
     <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
       <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
@@ -60,7 +58,7 @@
   </outputs>
     <tests>
         <test>
-            <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
             <param name="analysis_type_selector" value="-mapped"/>
             <output name="report">
               <assert_contents>
@@ -68,7 +66,7 @@
               </assert_contents>
               <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
             </output>
-            
+
         </test>
     </tests>
 <help>
@@ -89,19 +87,19 @@
 **How it works**
 
 The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
- 
+
   Mapping status (-mapped)          split mapped/unmapped and generate two output files
                                     named (MAPPED) and (UNMAPPED) containing mapped and unmapped
                                     reads, respectively.
-                                    
+
   Pairing status (-paired)          split single-end/paired-end alignments and generate two output files
                                     named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
                                     reads, respectively.
-                                    
+
   Reference name (-reference)       split alignments by reference name. In cases of unfinished genomes with
                                     very large number of reference sequences (scaffolds) it can generate
                                     thousands (if not millions) of output datasets.
-                                    
+
   Specific tag (-tag)               split alignments based on all values of TAG encountered. Choosing this
                                     option from the menu will allow you to enter the tag name. As was the
                                     case with the reference splitting above, this option can produce very