diff tools/clc_assembly_cell/clc_assembler.xml @ 4:46a667b5e19e draft

v0.0.6 update optional/required parameters and URLS in docs
author peterjc
date Wed, 01 Feb 2017 07:05:09 -0500
parents 139b6f0a0bb5
children 31a9169b6222
line wrap: on
line diff
--- a/tools/clc_assembly_cell/clc_assembler.xml	Wed May 11 06:49:58 2016 -0400
+++ b/tools/clc_assembly_cell/clc_assembler.xml	Wed Feb 01 07:05:09 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>