changeset 1:cab3f8d35989 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

--- a/macros.xml	Tue Apr 21 17:41:18 2015 -0400
+++ b/macros.xml	Tue May 09 11:18:12 2017 -0400
@@ -1,16 +1,17 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="1.3.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+                url = {https://samtools.github.io/hts-specs/},}
             </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
             <citation type="doi">10.1093/bioinformatics/btr076</citation>
@@ -41,7 +42,7 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -64,7 +65,5 @@
 5. Click **Save**
 
 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
     </token>
-
 </macros>

--- a/samtools_sort.xml	Tue Apr 21 17:41:18 2015 -0400
+++ b/samtools_sort.xml	Tue May 09 11:18:12 2017 -0400
@@ -1,12 +1,20 @@
-<tool id="samtools_sort" name="Sort" version="2.0">
-    <description>BAM dataset</description>
+<tool id="samtools_sort" name="Sort" version="2.0.1">
+    <description>order of storing aligned sequences</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
-    <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        samtools sort
+            $sort_mode
+            -@ \${GALAXY_SLOTS:-1}
+            -o '${output1}'
+            -O bam
+            -T dataset
+            '${input1}'
+    ]]></command>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM File" />
         <param name="sort_mode" type="select" label="Sort by ">
@@ -29,12 +37,9 @@
         </test>
     </tests>
     <help>
-
 **What it does**
 
 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
-
-
     </help>
-    <expand macro="citations"></expand>
+    <expand macro="citations"/>
 </tool>

--- a/tool_dependencies.xml	Tue Apr 21 17:41:18 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>