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comparison tools/clc_assembly_cell/clc_mapper.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_mapper" name="CLC Mapper" version="0.0.2"> 1 <tool id="clc_mapper" name="CLC Mapper" version="0.0.3">
2 <description>Maps reads giving a SAM/BAM file</description> 2 <description>Maps reads giving a SAM/BAM file</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">clc_mapper</requirement> 4 <requirement type="binary">clc_mapper</requirement>
5 <requirement type="binary">clc_cas_to_sam</requirement> 5 <requirement type="binary">clc_cas_to_sam</requirement>
6 <requirement type="binary">samtools</requirement> 6 <requirement type="binary">samtools</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement> 7 <requirement type="package" version="0.1.19">samtools</requirement>
8 </requirements> 8 </requirements>
9 <stdio>
10 <!-- Assume anything other than zero is an error -->
11 <exit_code range="1:" />
12 <exit_code range=":-1" />
13 </stdio>
9 <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command> 14 <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command>
10 <command>echo Mapping reads with clc_mapper... 15 <command>echo Mapping reads with clc_mapper...
11 &amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper 16 &amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper
12 #for $ref in $references 17 #for $ref in $references
13 #if str($ref.ref_type)=="circular" 18 #if str($ref.ref_type)=="circular"
49 &amp;&amp; echo Sorting BAM file with samtools... 54 &amp;&amp; echo Sorting BAM file with samtools...
50 &amp;&amp; samtools sort "temp_job.bam" "temp_sorted" 55 &amp;&amp; samtools sort "temp_job.bam" "temp_sorted"
51 &amp;&amp; mv "temp_sorted.bam" "$out_bam" 56 &amp;&amp; mv "temp_sorted.bam" "$out_bam"
52 &amp;&amp; echo Indexing BAM file with samtools... 57 &amp;&amp; echo Indexing BAM file with samtools...
53 &amp;&amp; samtools index "$out_bam"</command> 58 &amp;&amp; samtools index "$out_bam"</command>
54 <stdio>
55 <!-- Assume anything other than zero is an error -->
56 <exit_code range="1:" />
57 <exit_code range=":-1" />
58 </stdio>
59 <!-- Job splitting with merge via clc_join_mappings? --> 59 <!-- Job splitting with merge via clc_join_mappings? -->
60 <inputs> 60 <inputs>
61 <!-- Support linear and circular references (-z) --> 61 <!-- Support linear and circular references (-z) -->
62 <repeat name="references" title="Reference Sequence" min="1"> 62 <repeat name="references" title="Reference Sequence" min="1">
63 <param name="ref_file" type="data" format="fasta" required="true" label="Reference sequence(s) (FASTA)" /> 63 <param name="ref_file" type="data" format="fasta" required="true" label="Reference sequence(s) (FASTA)" />
161 cite this wrapper as: 161 cite this wrapper as:
162 162
163 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio 163 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
164 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell 164 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
165 165
166 CLC Assembly Cell, CLC bio (2008--2015)
167 http://www.clcbio.com/products/clc-assembly-cell/
168
166 This wrapper is available to install into other Galaxy Instances via the Galaxy 169 This wrapper is available to install into other Galaxy Instances via the Galaxy
167 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell 170 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
168 </help> 171 </help>
172 <citations>
173 <citation type="bibtex">
174 @MISC{clcbio,
175 AUTHOR = {CLC Bio}
176 title = {{CLC Assembly Cell}},
177 url = {http://www.clcbio.com/products/clc-assembly-cell/},
178 year = {2008--2015}
179 }
180 </citation>
181 </citations>
169 </tool> 182 </tool>