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Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>.
author crs4
date Thu, 06 Nov 2014 13:20:15 -0500
parents 6adb6e16b00f
children
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0:6adb6e16b00f 1:1fea05cdc1a1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.0.0"> 2 <tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.2.28.0">
3 <description/> 3 <description/>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.2.26">mosaik</requirement> 5 <requirement type="package" version="2.2.28">mosaik</requirement>
6 <requirement type="package" version="0.1.19">samtools</requirement> 6 <requirement type="package" version="0.1.19">samtools</requirement>
7 </requirements> 7 </requirements>
8 <version_command>MosaikJump | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | sed -n 's/MosaikJump \([[:digit:].]\{1,\}\).*/\1/p'</version_command> 8 <version_command>MosaikJump | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | sed -n 's/MosaikJump \([[:digit:].]\{1,\}\).*/\1/p'</version_command>
9 <command> 9 <command>
10 MosaikBuild -fr 10 MosaikBuild -fr
21 -q2 ${paired.reads2} 21 -q2 ${paired.reads2}
22 -mfl ${paired.mfl} 22 -mfl ${paired.mfl}
23 #set $ls_string = '-ls %s' % $paired.ls 23 #set $ls_string = '-ls %s' % $paired.ls
24 #end if 24 #end if
25 -st $st -out mosaik_reads_file; 25 -st $st -out mosaik_reads_file;
26 MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.26.pe.100.0065.ann -annse \$MOSAIK_NETWORK_DIR/2.1.26.se.100.005.ann $ls_string 26 MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.78.pe.ann -annse \$MOSAIK_NETWORK_DIR/2.1.78.se.ann $ls_string
27 #if str($mm) 27 #if str($mm)
28 -mm $mm 28 -mm $mm
29 #end if 29 #end if
30 #if str($act) 30 #if str($act)
31 -act $act 31 -act $act
34 -bw $bw 34 -bw $bw
35 #end if 35 #end if
36 #if str($mhp) 36 #if str($mhp)
37 -mhp $mhp 37 -mhp $mhp
38 #end if 38 #end if
39 -hs 15; 39 -hs 15 &amp;&amp;
40 #if str($outFormat) == 'bam' 40 #if str($outFormat) == 'bam'
41 samtools sort -o mosaik_aligned_file.bam out_prefix &gt; $output 41 samtools sort -o mosaik_aligned_file.bam out_prefix &gt; $output
42 #else 42 #else
43 samtools view mosaik_aligned_file.bam -o $output 43 samtools view mosaik_aligned_file.bam -o $output
44 #end if 44 #end if
139 This Galaxy tool is Copyright © 2005-2013 Pennsylvania State University, © 2013-2014 `CRS4 Srl.`_ and is released under the `Academic Free License v. 3.0`_. 139 This Galaxy tool is Copyright © 2005-2013 Pennsylvania State University, © 2013-2014 `CRS4 Srl.`_ and is released under the `Academic Free License v. 3.0`_.
140 140
141 .. _CRS4 Srl.: http://www.crs4.it/ 141 .. _CRS4 Srl.: http://www.crs4.it/
142 .. _Academic Free License v. 3.0: http://opensource.org/licenses/AFL-3.0 142 .. _Academic Free License v. 3.0: http://opensource.org/licenses/AFL-3.0
143 143
144 If you use this tool in Galaxy, please cite |Cuccuru2014|_. 144 You can use this tool only if you agree to the license terms of: `MOSAIK`_.
145
146 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
147 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135
148
149 This tool uses `MOSAIK`_, which is licensed separately. Please cite |Lee2014|_.
150 145
151 .. _MOSAIK: https://code.google.com/p/mosaik-aligner/ 146 .. _MOSAIK: https://code.google.com/p/mosaik-aligner/
147
148 If you use this tool, please cite:
149
150 - |Cuccuru2014|_
151 - |Lee2014|_.
152
153 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
154 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
152 .. |Lee2014| replace:: Lee, W.-P., *et al.* (2014) MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. *PLoS ONE* 9(3), e90581 155 .. |Lee2014| replace:: Lee, W.-P., *et al.* (2014) MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. *PLoS ONE* 9(3), e90581
153 .. _Lee2014: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090581 156 .. _Lee2014: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090581
154 </help> 157 </help>
158 <citations>
159 <citation type="doi">10.1093/bioinformatics/btu135</citation>
160 <citation type="doi">10.1371/journal.pone.0090581</citation>
161 </citations>
155 </tool> 162 </tool>