Mercurial > repos > devteam > sam_to_bam
annotate sam_to_bam.xml @ 3:ab4c4e07eb3c
Fix for using built-in reference data.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 17 Jan 2014 16:30:43 -0500 |
| parents | 93f2e3337a33 |
| children | 8176b2575aa1 |
| rev | line source |
|---|---|
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1
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
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> | |
| 4 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 sam_to_bam.py | |
| 8 --input1=$source.input1 | |
| 9 #if $source.index_source == "history": | |
| 10 --ref_file=$source.ref_file | |
| 11 #else | |
|
1
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
12 --index=${source.index.fields.path} |
| 0 | 13 #end if |
| 14 --output1=$output1 | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <conditional name="source"> | |
| 18 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 19 <option value="cached">Locally cached</option> | |
| 20 <option value="history">History</option> | |
| 21 </param> | |
| 22 <when value="cached"> | |
|
1
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
23 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert"> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
24 <validator type="unspecified_build" /> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
25 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
26 </param> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
27 <param name="index" type="select" label="Using reference genome"> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
28 <options from_data_table="fasta_indexes"> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
29 <filter type="data_meta" ref="input1" key="dbkey" column="1" /> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
30 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> |
|
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
31 </options> |
| 0 | 32 </param> |
| 33 </when> | |
| 34 <when value="history"> | |
|
1
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
35 <param name="input1" type="data" format="sam" label="SAM file to convert" /> |
| 0 | 36 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /> |
| 37 </when> | |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM"> | |
| 42 <actions> | |
| 43 <conditional name="source.index_source"> | |
| 44 <when value="cached"> | |
| 45 <action type="metadata" name="dbkey"> | |
| 46 <option type="from_param" name="source.input1" param_attribute="dbkey" /> | |
| 47 </action> | |
| 48 </when> | |
| 49 <when value="history"> | |
| 50 <action type="metadata" name="dbkey"> | |
| 51 <option type="from_param" name="source.ref_file" param_attribute="dbkey" /> | |
| 52 </action> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 </actions> | |
| 56 </data> | |
| 57 </outputs> | |
| 58 <tests> | |
| 59 <test> | |
| 60 <!-- | |
| 61 Sam-to-Bam command: | |
| 62 cp test-data/chr_m.fasta . | |
| 63 samtools faidx chr_m.fasta | |
| 64 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam | |
| 65 samtools sort unsorted.bam sam_to_bam_out1 | |
| 66 chr_m.fasta is the reference file (chrM from equCab2) | |
| 67 --> | |
| 68 <param name="index_source" value="history" /> | |
| 69 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /> | |
| 70 <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> | |
| 71 <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" /> | |
| 72 </test> | |
| 73 <test> | |
| 74 <!-- | |
| 75 Sam-to-Bam command: | |
| 76 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam | |
| 77 samtools sort unsorted.bam sam_to_bam_out2 | |
| 78 chr_m.fasta is the reference file and the index chr_m.fasta.fai | |
| 79 these should be in the same directory, and chrM is from equCab2 | |
| 80 --> | |
| 81 <param name="index_source" value="cached" /> | |
| 82 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> | |
|
1
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
83 <param name="index" value="chr_m" /> |
| 0 | 84 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /> |
| 85 </test> | |
| 86 </tests> | |
| 87 <help> | |
| 88 | |
| 89 **What it does** | |
| 90 | |
| 91 This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. | |
| 92 | |
| 93 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
| 94 | |
| 95 ------ | |
| 96 | |
| 97 **Citation** | |
| 98 | |
| 99 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>`_ | |
| 100 | |
| 101 </help> | |
| 102 </tool> |