# HG changeset patch
# User peterjc
# Date 1485950666 18000
# Node ID b57f1d59f791c0609bc7eac261daadec8a5c8695
# Parent  60ade555476f763fc8e0d2db77ad4cbc4fe323a4
v0.0.6 update optional/required parameters and URLS in docs

diff -r 60ade555476f -r b57f1d59f791 tools/clc_assembly_cell/README.rst
--- a/tools/clc_assembly_cell/README.rst	Wed May 11 06:48:51 2016 -0400
+++ b/tools/clc_assembly_cell/README.rst	Wed Feb 01 07:04:26 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
 ==========================================================
 
-This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2013-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -93,6 +93,8 @@
           unmapped reads in the CLC Mapper wrapper.
         - Bug fix to use the ``$CLC_ASSEMBLY_CELL`` environment variable when
           calling ``clc_cas_to_sam`` in the CLC MApper wrapper.
+v0.0.6  - Update tool XML for optional vs required parameters.
+        - Update URLs in documentation.
 ======= ======================================================================
 
 
diff -r 60ade555476f -r b57f1d59f791 tools/clc_assembly_cell/clc_assembler.xml
--- a/tools/clc_assembly_cell/clc_assembler.xml	Wed May 11 06:48:51 2016 -0400
+++ b/tools/clc_assembly_cell/clc_assembler.xml	Wed Feb 01 07:04:26 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="clc_assembler" name="CLC assembler" version="0.0.4">
+<tool id="clc_assembler" name="CLC assembler" version="0.0.6">
     <description>Assembles reads giving a FASTA file</description>
     <requirements>
         <requirement type="binary">clc_assembler</requirement>
@@ -58,8 +58,8 @@
                            label="Minimum size of 'good' DNA templates in the library preparation" />
                     <param name="max_size" type="integer" optional="false" min="0" value=""
                            label="Maximum size of 'good' DNA templates in the library preparation" />
-                    <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/>
-                    <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
+                    <param name="filename1" type="data" format="fastq,fasta" label="Read file one"/>
+                    <param name="filename2" type="data" format="fastq,fasta" label="Read file two"/>
                 </when>
                 <when value="interleaved">
                     <param name="placement" type="select" label="Pairing type (segment placing)">
@@ -79,10 +79,10 @@
                            label="Minimum size of 'good' DNA templates in the library preparation" />
                     <param name="max_size" type="integer" optional="false" min="0" value=""
                            label="Maximum size of 'good' DNA templates in the library preparation" />
-                    <param name="filename" type="data" format="fastq,fasta" required="true" label="Interleaved read file"/>
+                    <param name="filename" type="data" format="fastq,fasta" label="Interleaved read file"/>
                 </when>
                 <when value="none">
-                    <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)"
+                    <param name="filenames" type="data" format="fastq,fasta" multiple="true" optional="false" label="Read file(s)"
                            help="Multiple files allowed, for example several files of orphan reads." />
                 </when>
             </conditional>
@@ -128,7 +128,7 @@
 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
 
 CLC Assembly Cell, CLC bio (2008--2015)
-http://www.clcbio.com/products/clc-assembly-cell/
+https://www.qiagenbioinformatics.com/products/clc-assembly-cell/
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
@@ -138,7 +138,7 @@
 @MISC{clcbio,
 AUTHOR = {CLC Bio}
 title ={{CLC Assembly Cell}},
-url = {http://www.clcbio.com/products/clc-assembly-cell/},
+url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/},
 year = {2008--2015}
 }
         </citation>
diff -r 60ade555476f -r b57f1d59f791 tools/clc_assembly_cell/clc_mapper.xml
--- a/tools/clc_assembly_cell/clc_mapper.xml	Wed May 11 06:48:51 2016 -0400
+++ b/tools/clc_assembly_cell/clc_mapper.xml	Wed Feb 01 07:04:26 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="clc_mapper" name="CLC Mapper" version="0.0.5">
+<tool id="clc_mapper" name="CLC Mapper" version="0.0.6">
     <description>Maps reads giving a SAM/BAM file</description>
     <requirements>
         <requirement type="binary">clc_mapper</requirement>    
@@ -64,7 +64,7 @@
     <inputs>
         <!-- Support linear and circular references (-z) -->
         <repeat name="references" title="Reference Sequence" min="1">
-            <param name="ref_file" type="data" format="fasta" required="true" label="Reference sequence(s) (FASTA)" />
+            <param name="ref_file" type="data" format="fasta" label="Reference sequence(s) (FASTA)" />
             <param name="ref_type" type="select" label="Reference type">
                 <option value="linear">Linear (e.g. most chromosomes)</option>
                 <option value="circular">Circular (e.g. bacterial chromosomes, mitochondria)</option>
@@ -95,9 +95,9 @@
                            label="Minimum size of 'good' DNA templates in the library preparation" />
                     <param name="max_size" type="integer" optional="false" min="0" value=""
                            label="Maximum size of 'good' DNA templates in the library preparation" />
-                    <param name="filename1" type="data" format="fastqsanger,fasta" required="true" label="Read file one"
+                    <param name="filename1" type="data" format="fastqsanger,fasta" label="Read file one"
                            help="FASTA or Sanger FASTQ accepted." />
-                    <param name="filename2" type="data" format="fastqsanger,fasta" required="true" label="Read file two"
+                    <param name="filename2" type="data" format="fastqsanger,fasta" label="Read file two"
                            help="FASTA or Sanger FASTQ accepted." />
                 </when>
                 <when value="interleaved">
@@ -118,11 +118,11 @@
                            label="Minimum size of 'good' DNA templates in the library preparation" />
                     <param name="max_size" type="integer" optional="false" min="0" value=""
                            label="Maximum size of 'good' DNA templates in the library preparation" />
-                    <param name="filename" type="data" format="fastqsanger,fasta" required="true" label="Interleaved read file"
+                    <param name="filename" type="data" format="fastqsanger,fasta" label="Interleaved read file"
                            help="FASTA or Sanger FASTQ accepted."/>
                 </when>
                 <when value="none">
-                    <param name="filenames" type="data" format="fastqsanger,fasta" multiple="true" required="true" label="Read file(s)"
+                    <param name="filenames" type="data" format="fastqsanger,fasta" multiple="true" optional="false" label="Read file(s)"
                            help="Multiple files allowed, for example several files of orphan reads. FASTA or Sanger FASTQ accepted." />
                 </when>
             </conditional>
@@ -182,7 +182,7 @@
 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
 
 CLC Assembly Cell, CLC bio (2008--2015)
-http://www.clcbio.com/products/clc-assembly-cell/
+https://www.qiagenbioinformatics.com/products/clc-assembly-cell/
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
@@ -192,7 +192,7 @@
 @MISC{clcbio,
 AUTHOR = {CLC Bio} 
 title = {{CLC Assembly Cell}},
-url = {http://www.clcbio.com/products/clc-assembly-cell/},
+url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/},
 year = {2008--2015}
 }
         </citation>
diff -r 60ade555476f -r b57f1d59f791 tools/clc_assembly_cell/tool_dependencies.xml
--- a/tools/clc_assembly_cell/tool_dependencies.xml	Wed May 11 06:48:51 2016 -0400
+++ b/tools/clc_assembly_cell/tool_dependencies.xml	Wed Feb 01 07:04:26 2017 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>