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changeset 1:4555f451dd79 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:34:02 -0500
parents 71dd32fb0b0a
children e2c1b62e1db1
files bamtools-split.xml shed_upload.tar.gz tool_dependencies.xml
diffstat 3 files changed, 24 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/bamtools-split.xml	Fri Jan 09 11:50:08 2015 -0500
+++ b/bamtools-split.xml	Wed Nov 11 12:34:02 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>
@@ -44,12 +42,15 @@
         <option value="-reference">Reference name (-reference)</option>
         <option value="-tag">Specific tag (-tag)</option>
       </param>
+      <when value="-mapped" />
+      <when value="-paired" />
+      <when value="-reference" />
       <when value="-tag">
         <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter &quot;NM&quot;"/>
       </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"/>
@@ -57,7 +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>
@@ -65,7 +66,7 @@
               </assert_contents>
               <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
             </output>
-            
+
         </test>
     </tests>
 <help>
@@ -86,19 +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
Binary file shed_upload.tar.gz has changed
--- a/tool_dependencies.xml	Fri Jan 09 11:50:08 2015 -0500
+++ b/tool_dependencies.xml	Wed Nov 11 12:34:02 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="bamtools" version="2.3.0_2d7685d2ae">
-        <repository changeset_revision="4e49af060657" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>