# HG changeset patch
# User devteam
# Date 1484757874 18000
# Node ID 64ed37303c15e588c4b18f82e5c785197deecf50
# Parent  10dcc80277785b69b658ad65c1a52e1d5d70e350
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01

diff -r 10dcc8027778 -r 64ed37303c15 bamtools-split.xml
--- a/bamtools-split.xml	Mon Nov 09 12:04:47 2015 -0500
+++ b/bamtools-split.xml	Wed Jan 18 11:44:34 2017 -0500
@@ -1,75 +1,63 @@
-<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>
-  </requirements>
-  <command>
-
-    echo "BAM" > $report &amp;&amp;
-
-    #for $bam_count, $input_bam in enumerate( $input_bams ):
-      ln -s "${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>
-    <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>
-        <option value="-paired">Pairing status (-paired)</option>
-        <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"/>
-    </data>
-  </outputs>
+<tool id="bamSplit" name="Split" version="2.4.0">
+    <description>BAM datasets on variety of attributes</description>
+    <requirements>
+        <requirement type="package" version="2.4.0">bamtools</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            echo "BAM" > $report &&
+            #for $bam_count, $input_bam in enumerate( $input_bams ):
+                ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
+                ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
+            #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>
+        <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>
+                <option value="-paired">Pairing status (-paired)</option>
+                <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"/>
+        </data>
+    </outputs>
     <tests>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
             <param name="analysis_type_selector" value="-mapped"/>
             <output name="report">
-              <assert_contents>
-                <has_line line="BAM" />
-              </assert_contents>
-              <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
+                <assert_contents>
+                    <has_line line="BAM" />
+                </assert_contents>
+                <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
             </output>
-
         </test>
     </tests>
-<help>
+    <help>
 **What is does**
 
 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
@@ -113,8 +101,8 @@
 
 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
 
-</help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btr174</citation>
-  </citations>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr174</citation>
+    </citations>
 </tool>
diff -r 10dcc8027778 -r 64ed37303c15 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 12:04:47 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bamtools" version="2.3.0_2d7685d2ae">
-        <repository changeset_revision="f1ce7a19eb68" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>