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comparison tools/clc_assembly_cell/clc_assembler.xml @ 2:139b6f0a0bb5 draft

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v0.0.4 fix recording of clc version
author peterjc
date Tue, 01 Sep 2015 06:55:13 -0400
parents 5ae1c0312aaa
children 46a667b5e19e
comparison
equal deleted inserted replaced
1:5ae1c0312aaa 2:139b6f0a0bb5
1 <tool id="clc_assembler" name="CLC assembler" version="0.0.3"> 1 <tool id="clc_assembler" name="CLC assembler" version="0.0.4">
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> 6 <stdio>
7 <!-- Assume anything other than zero is an error --> 7 <!-- Assume anything other than zero is an error -->
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
10 </stdio> 10 </stdio>
11 <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>
12 <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
13 #for $rg in $read_group 13 #for $rg in $read_group
14 ##-------------------------------------- 14 ##--------------------------------------
15 #if str($rg.segments.type) == "paired" 15 #if str($rg.segments.type) == "paired"
16 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2" 16 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"