Mercurial > repos > devteam > sam_to_bam
annotate sam_to_bam.xml @ 1:7095d651c95f draft
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
| author | devteam |
|---|---|
| date | Thu, 27 Mar 2014 14:04:25 -0400 |
| parents | d59a7ac34414 |
| children | 5a5f92086188 |
| rev | line source |
|---|---|
|
1
7095d651c95f
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
devteam
parents:
0
diff
changeset
|
1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3"> |
| 0 | 2 <description>converts SAM format to BAM format</description> |
| 3 <requirements> | |
|
1
7095d651c95f
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
devteam
parents:
0
diff
changeset
|
4 <requirement type="package" version="0.1.19">samtools</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python"> | |
| 7 sam_to_bam.py | |
| 8 --input1=$source.input1 | |
| 9 #if $source.index_source == "history": | |
| 10 --dbkey=${ref_file.metadata.dbkey} | |
| 11 --ref_file=$source.ref_file | |
| 12 #else | |
| 13 --dbkey=${input1.metadata.dbkey} | |
| 14 #end if | |
| 15 --output1=$output1 | |
| 16 --index_dir=${GALAXY_DATA_INDEX_DIR} | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <conditional name="source"> | |
| 20 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 21 <option value="cached">Locally cached</option> | |
| 22 <option value="history">History</option> | |
| 23 </param> | |
| 24 <when value="cached"> | |
| 25 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"> | |
| 26 <validator type="unspecified_build" /> | |
| 27 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> | |
| 28 </param> | |
| 29 </when> | |
| 30 <when value="history"> | |
| 31 <param name="input1" type="data" format="sam" label="Convert SAM file" /> | |
| 32 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /> | |
| 33 </when> | |
| 34 </conditional> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM"> | |
| 38 <actions> | |
| 39 <conditional name="source.index_source"> | |
| 40 <when value="cached"> | |
| 41 <action type="metadata" name="dbkey"> | |
| 42 <option type="from_param" name="source.input1" param_attribute="dbkey" /> | |
| 43 </action> | |
| 44 </when> | |
| 45 <when value="history"> | |
| 46 <action type="metadata" name="dbkey"> | |
| 47 <option type="from_param" name="source.ref_file" param_attribute="dbkey" /> | |
| 48 </action> | |
| 49 </when> | |
| 50 </conditional> | |
| 51 </actions> | |
| 52 </data> | |
| 53 </outputs> | |
| 54 <tests> | |
| 55 <test> | |
| 56 <!-- | |
| 57 Sam-to-Bam command: | |
| 58 cp test-data/chr_m.fasta . | |
| 59 samtools faidx chr_m.fasta | |
| 60 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam | |
| 61 samtools sort unsorted.bam sam_to_bam_out1 | |
| 62 chr_m.fasta is the reference file (chrM from equCab2) | |
| 63 --> | |
| 64 <param name="index_source" value="history" /> | |
| 65 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /> | |
| 66 <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> | |
| 67 <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" /> | |
| 68 </test> | |
| 69 <test> | |
| 70 <!-- | |
| 71 Sam-to-Bam command: | |
| 72 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam | |
| 73 samtools sort unsorted.bam sam_to_bam_out2 | |
| 74 chr_m.fasta is the reference file and the index chr_m.fasta.fai | |
| 75 these should be in the same directory, and chrM is from equCab2 | |
| 76 --> | |
| 77 <param name="index_source" value="cached" /> | |
| 78 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> | |
| 79 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /> | |
| 80 </test> | |
| 81 </tests> | |
| 82 <help> | |
| 83 | |
| 84 **What it does** | |
| 85 | |
| 86 This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. | |
| 87 | |
| 88 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
| 89 | |
| 90 ------ | |
| 91 | |
| 92 **Citation** | |
| 93 | |
| 94 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | |
| 95 | |
| 96 </help> | |
| 97 </tool> |