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changeset 6:eac9d3319326 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:17:29 -0400
parents 4ffbc8cedb42
children fbf3f04324a1
files bam_to_sam.xml macros.xml tool_dependencies.xml
diffstat 3 files changed, 29 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- a/bam_to_sam.xml	Fri Dec 18 19:42:16 2015 -0500
+++ b/bam_to_sam.xml	Tue May 09 11:17:29 2017 -0400
@@ -1,21 +1,23 @@
-<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="version_command"></expand>
-  <expand macro="stdio"></expand>
-  <description>convert BAM to SAM</description>  
-    <command>
-<![CDATA[
-  samtools view -o "${output1}" ${header} "${input1}"
-]]>
-    </command>
+<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.1">
+    <description>convert BAM to SAM</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+        samtools view -o '${output1}' ${header} '${input1}'
+    ]]></command>
+
     <inputs>
-        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
-        <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
+        <param format="bam" name="input1" type="data" label="BAM File to Convert" />
+        <param name="header" label="Header options" type="select"
+               help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
           <option value="-h">Include header in SAM output (-h)</option>
-          <option value="-H">Print header only (-H)</option>
+          <option value="-H">Return header only (-H)</option>
           <option value="">Exclude header</option>
         </param>
     </inputs>
@@ -26,29 +28,23 @@
         <test>
             <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
             <param name="header" value="-h" />
-            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
+            <output file="bam_to_sam_out1.sam" name="output1" />
         </test>
         <test>
             <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
             <param name="header" value="-H" />
-            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
+            <output file="bam_to_sam_out2.sam" name="output1" />
         </test>
         <test>
             <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
             <param name="header" value="" />
-            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
+            <output file="bam_to_sam_out3.sam" name="output1" />
         </test>
     </tests>
-    <help>
-<![CDATA[
-
+    <help><![CDATA[
 **What it does**
 
-Converts BAM dataset to SAM using ``samtools view`` command::
-
- samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] 
-
-]]>
-  </help>
-  <expand macro="citations"></expand>
+Converts BAM dataset to SAM using the ``samtools view`` command.
+    ]]></help>
+    <expand macro="citations"/>
 </tool>
--- a/macros.xml	Fri Dec 18 19:42:16 2015 -0500
+++ b/macros.xml	Tue May 09 11:17:29 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>echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?")</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/tool_dependencies.xml	Fri Dec 18 19:42:16 2015 -0500
+++ /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="a55970300738" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>