Mercurial > repos > crs4 > mosaik2
annotate mosaik2.xml @ 1:1fea05cdc1a1 draft default tip
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 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
|
1
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
2 <tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.2.28.0"> |
| 0 | 3 <description/> |
| 4 <requirements> | |
|
1
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
5 <requirement type="package" version="2.2.28">mosaik</requirement> |
| 0 | 6 <requirement type="package" version="0.1.19">samtools</requirement> |
| 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> | |
| 9 <command> | |
| 10 MosaikBuild -fr | |
| 11 #if $genomeSource.refGenomeSource == 'indexed' | |
| 12 ${genomeSource.indexReference.fields.path} | |
| 13 #else | |
| 14 ${genomeSource.historyReference} | |
| 15 #end if | |
| 16 -oa mosaik_ref_file; | |
| 17 MosaikBuild -q $reads | |
| 18 #if $paired.kind == 'single' | |
| 19 #set $ls_string = '' | |
| 20 #else | |
| 21 -q2 ${paired.reads2} | |
| 22 -mfl ${paired.mfl} | |
| 23 #set $ls_string = '-ls %s' % $paired.ls | |
| 24 #end if | |
| 25 -st $st -out mosaik_reads_file; | |
|
1
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
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 $ls_string |
| 0 | 27 #if str($mm) |
| 28 -mm $mm | |
| 29 #end if | |
| 30 #if str($act) | |
| 31 -act $act | |
| 32 #end if | |
| 33 #if str($bw) | |
| 34 -bw $bw | |
| 35 #end if | |
| 36 #if str($mhp) | |
| 37 -mhp $mhp | |
| 38 #end if | |
|
1
1fea05cdc1a1
Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>.
crs4
parents:
0
diff
changeset
|
39 -hs 15 && |
| 0 | 40 #if str($outFormat) == 'bam' |
| 41 samtools sort -o mosaik_aligned_file.bam out_prefix > $output | |
| 42 #else | |
| 43 samtools view mosaik_aligned_file.bam -o $output | |
| 44 #end if | |
| 45 </command> | |
| 46 <inputs> | |
| 47 <conditional name="genomeSource"> | |
| 48 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> | |
| 49 <option value="indexed">Use a built-in index</option> | |
| 50 <option value="history">Use one from the history</option> | |
| 51 </param> | |
| 52 <when value="indexed"> | |
| 53 <param name="indexReference" type="select" label="Select a reference genome"> | |
| 54 <options from_data_table="mosaik_indexes"> | |
| 55 <filter type="sort_by" column="2" /> | |
| 56 <validator type="no_options" message="No indexes are available" /> | |
| 57 </options> | |
| 58 </param> | |
| 59 </when> | |
| 60 <when value="history"> | |
| 61 <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history" /> | |
| 62 </when> | |
| 63 </conditional> | |
| 64 <param name="st" type="select" label="Sequencing technology used"> | |
| 65 <option value="454">454</option> | |
| 66 <option value="illumina">Illumina</option> | |
| 67 <option value="solid">Solid</option> | |
| 68 <option value="sanger">Sanger</option> | |
| 69 <option value="helicos">Helicos</option> | |
| 70 </param> | |
| 71 <param format="fastq" name="reads" type="data" label="FASTQ reads file" /> | |
| 72 <conditional name="paired"> | |
| 73 <param name="kind" type="select" label="Is this library mate-paired?"> | |
| 74 <option value="single">Single-end</option> | |
| 75 <option value="paired">Paired-end</option> | |
| 76 </param> | |
| 77 <when value="single" /> | |
| 78 <when value="paired"> | |
| 79 <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" /> | |
| 80 <param name="mfl" type="integer" value="200" label="Median fragment length" /> | |
| 81 <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /> | |
| 82 </when> | |
| 83 </conditional> | |
| 84 <param name="mm" type="integer" value="6" optional="true" label="Number of mismatches allowed per sequence" /> | |
| 85 <param name="act" type="integer" value="35" optional="true" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" /> | |
| 86 <param name="bw" type="integer" value="9" optional="true" label="Smith-Waterman band width" /> | |
| 87 <param name="mhp" type="integer" value="100" optional="true" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /> | |
| 88 <param name="outFormat" type="select" label="Output format"> | |
| 89 <option value="sam">SAM</option> | |
| 90 <option value="bam">BAM</option> | |
| 91 </param> | |
| 92 </inputs> | |
| 93 <outputs> | |
| 94 <data format="sam" name="output"> | |
| 95 <change_format> | |
| 96 <when input="outFormat" value="bam" format="bam" /> | |
| 97 </change_format> | |
| 98 <actions> | |
| 99 <conditional name="genomeSource.refGenomeSource"> | |
| 100 <when value="indexed"> | |
| 101 <action type="metadata" name="dbkey"> | |
| 102 <option type="from_data_table" name="mosaik_indexes" column="1"> | |
| 103 <filter type="param_value" column="0" value="#" compare="startswith" keep="False" /> | |
| 104 <filter type="param_value" ref="genomeSource.indexReference" column="0" /> | |
| 105 </option> | |
| 106 </action> | |
| 107 </when> | |
| 108 <when value="history"> | |
| 109 <action type="metadata" name="dbkey"> | |
| 110 <option type="from_param" name="genomeSource.historyReference" param_attribute="dbkey" /> | |
| 111 </action> | |
| 112 </when> | |
| 113 </conditional> | |
| 114 </actions> | |
| 115 </data> | |
| 116 </outputs> | |
| 117 <tests> | |
| 118 <test> | |
| 119 <param name="refGenomeSource" value="history" /> | |
| 120 <param name="historyReference" ftype="fasta" value="mosaik_test_ref.fasta" /> | |
| 121 <param name="st" value="454" /> | |
| 122 <param name="reads" ftype="fastq" value="mosaik_test_input.fastq" /> | |
| 123 <param name="kind" value="single" /> | |
| 124 <param name="mm" value="6" /> | |
| 125 <param name="act" value="35" /> | |
| 126 <param name="bw" value="9" /> | |
| 127 <param name="mhp" value="100" /> | |
| 128 <param name="outFormat" value="sam" /> | |
| 129 <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0" /> | |
| 130 </test> | |
| 131 </tests> | |
| 132 <help> | |
| 133 **What it does** | |
| 134 | |
| 135 This tool uses `MOSAIK`_ v. 2 to align reads to a reference sequence. | |
| 136 | |
| 137 **License and citation** | |
| 138 | |
| 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 | |
| 141 .. _CRS4 Srl.: http://www.crs4.it/ | |
| 142 .. _Academic Free License v. 3.0: http://opensource.org/licenses/AFL-3.0 | |
| 143 | |
|
1
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
144 You can use this tool only if you agree to the license terms of: `MOSAIK`_. |
| 0 | 145 |
| 146 .. _MOSAIK: https://code.google.com/p/mosaik-aligner/ | |
|
1
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
147 |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
148 If you use this tool, please cite: |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
149 |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
150 - |Cuccuru2014|_ |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
151 - |Lee2014|_. |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
152 |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
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 |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
154 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 |
| 0 | 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 |
| 156 .. _Lee2014: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090581 | |
| 157 </help> | |
|
1
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
158 <citations> |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
159 <citation type="doi">10.1093/bioinformatics/btu135</citation> |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
160 <citation type="doi">10.1371/journal.pone.0090581</citation> |
|
1fea05cdc1a1
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>.
crs4
parents:
0
diff
changeset
|
161 </citations> |
| 0 | 162 </tool> |