# HG changeset patch
# User peterjc
# Date 1441104913 14400
# Node ID 139b6f0a0bb5807b40bab4abb92a7dc2d3ba6016
# Parent  5ae1c0312aaa7e97fa630e0cabc17cf74970275c
v0.0.4 fix recording of clc version

diff -r 5ae1c0312aaa -r 139b6f0a0bb5 tools/clc_assembly_cell/README.rst
--- a/tools/clc_assembly_cell/README.rst	Wed Aug 05 10:57:39 2015 -0400
+++ b/tools/clc_assembly_cell/README.rst	Tue Sep 01 06:55:13 2015 -0400
@@ -88,6 +88,7 @@
 v0.0.3  - Reorder XML elements (internal change only).
         - Added citation tags.
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.4  - Bug fix for ``<version_command>`` to capture tool version.
 ======= ======================================================================
 
 
@@ -101,12 +102,12 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
     ...
 
 To just build and check the tar ball, use::
diff -r 5ae1c0312aaa -r 139b6f0a0bb5 tools/clc_assembly_cell/clc_assembler.xml
--- a/tools/clc_assembly_cell/clc_assembler.xml	Wed Aug 05 10:57:39 2015 -0400
+++ b/tools/clc_assembly_cell/clc_assembler.xml	Tue Sep 01 06:55:13 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="clc_assembler" name="CLC assembler" version="0.0.3">
+<tool id="clc_assembler" name="CLC assembler" version="0.0.4">
     <description>Assembles reads giving a FASTA file</description>
     <requirements>
         <requirement type="binary">clc_assembler</requirement>
@@ -8,7 +8,7 @@
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
-    <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
+    <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
     <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
 #for $rg in $read_group
 ##--------------------------------------
diff -r 5ae1c0312aaa -r 139b6f0a0bb5 tools/clc_assembly_cell/clc_mapper.xml
--- a/tools/clc_assembly_cell/clc_mapper.xml	Wed Aug 05 10:57:39 2015 -0400
+++ b/tools/clc_assembly_cell/clc_mapper.xml	Tue Sep 01 06:55:13 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="clc_mapper" name="CLC Mapper" version="0.0.3">
+<tool id="clc_mapper" name="CLC Mapper" version="0.0.4">
     <description>Maps reads giving a SAM/BAM file</description>
     <requirements>
         <requirement type="binary">clc_mapper</requirement>    
@@ -11,7 +11,7 @@
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
-    <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command>
+    <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command>
     <command>echo Mapping reads with clc_mapper...
 &amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper
 #for $ref in $references