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comparison tools/clc_assembly_cell/clc_assembler.xml @ 1:5ae1c0312aaa draft

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v0.0.3 citation information and internal changes
author peterjc
date Wed, 05 Aug 2015 10:57:39 -0400
parents 0996169ac2e8
children 139b6f0a0bb5
comparison
equal deleted inserted replaced
0:0996169ac2e8 1:5ae1c0312aaa
1 <tool id="clc_assembler" name="CLC assembler" version="0.0.2"> 1 <tool id="clc_assembler" name="CLC assembler" version="0.0.3">
2 <description>Assembles reads giving a FASTA file</description> 2 <description>Assembles reads giving a FASTA file</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">clc_assembler</requirement> 4 <requirement type="binary">clc_assembler</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <!-- Assume anything other than zero is an error -->
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 </stdio>
6 <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> 11 <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
7 <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler 12 <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
8 #for $rg in $read_group 13 #for $rg in $read_group
9 ##-------------------------------------- 14 ##--------------------------------------
10 #if str($rg.segments.type) == "paired" 15 #if str($rg.segments.type) == "paired"
25 #end for 30 #end for
26 -m $min_contig_len 31 -m $min_contig_len
27 -o "$out_fasta" 32 -o "$out_fasta"
28 --cpus \${GALAXY_SLOTS:-4} 33 --cpus \${GALAXY_SLOTS:-4}
29 -v | grep -v "^Progress: "</command> 34 -v | grep -v "^Progress: "</command>
30 <stdio>
31 <!-- Assume anything other than zero is an error -->
32 <exit_code range="1:" />
33 <exit_code range=":-1" />
34 </stdio>
35 <inputs> 35 <inputs>
36 <repeat name="read_group" title="Read Group" min="1"> 36 <repeat name="read_group" title="Read Group" min="1">
37 <conditional name="segments"> 37 <conditional name="segments">
38 <param name="type" type="select" label="Are these paired reads?"> 38 <param name="type" type="select" label="Are these paired reads?">
39 <option value="paired">Paired reads (as two files)</option> 39 <option value="paired">Paired reads (as two files)</option>
125 cite this wrapper as: 125 cite this wrapper as:
126 126
127 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio 127 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
128 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell 128 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
129 129
130 CLC Assembly Cell, CLC bio (2008--2015)
131 http://www.clcbio.com/products/clc-assembly-cell/
132
130 This wrapper is available to install into other Galaxy Instances via the Galaxy 133 This wrapper is available to install into other Galaxy Instances via the Galaxy
131 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell 134 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
132 </help> 135 </help>
136 <citations>
137 <citation type="bibtex">
138 @MISC{clcbio,
139 AUTHOR = {CLC Bio}
140 title ={{CLC Assembly Cell}},
141 url = {http://www.clcbio.com/products/clc-assembly-cell/},
142 year = {2008--2015}
143 }
144 </citation>
145 </citations>
133 </tool> 146 </tool>