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Update sam_to_bam to use the fasta_indexes data table.
author Dave Bouvier <dave@bx.psu.edu>
date Wed, 11 Dec 2013 12:54:32 -0500
parents 30fdbaccb96b
children 8176b2575aa1
comparison
equal deleted inserted replaced
0:30fdbaccb96b 1:93f2e3337a33
1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2"> 1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3">
2 <description>converts SAM format to BAM format</description> 2 <description>converts SAM format to BAM format</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.18">samtools</requirement> 4 <requirement type="package" version="0.1.18">samtools</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 sam_to_bam.py 7 sam_to_bam.py
8 --input1=$source.input1 8 --input1=$source.input1
9 #if $source.index_source == "history": 9 #if $source.index_source == "history":
10 --dbkey=${ref_file.metadata.dbkey}
11 --ref_file=$source.ref_file 10 --ref_file=$source.ref_file
12 #else 11 #else
13 --dbkey=${input1.metadata.dbkey} 12 --index=${source.index.fields.path}
14 #end if 13 #end if
15 --output1=$output1 14 --output1=$output1
16 --index_dir=${GALAXY_DATA_INDEX_DIR}
17 </command> 15 </command>
18 <inputs> 16 <inputs>
19 <conditional name="source"> 17 <conditional name="source">
20 <param name="index_source" type="select" label="Choose the source for the reference list"> 18 <param name="index_source" type="select" label="Choose the source for the reference list">
21 <option value="cached">Locally cached</option> 19 <option value="cached">Locally cached</option>
22 <option value="history">History</option> 20 <option value="history">History</option>
23 </param> 21 </param>
24 <when value="cached"> 22 <when value="cached">
25 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"> 23 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert">
26 <validator type="unspecified_build" /> 24 <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" /> 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." />
26 </param>
27 <param name="index" type="select" label="Using reference genome">
28 <options from_data_table="fasta_indexes">
29 <filter type="data_meta" ref="input1" key="dbkey" column="1" />
30 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
31 </options>
28 </param> 32 </param>
29 </when> 33 </when>
30 <when value="history"> 34 <when value="history">
31 <param name="input1" type="data" format="sam" label="Convert SAM file" /> 35 <param name="input1" type="data" format="sam" label="SAM file to convert" />
32 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /> 36 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
33 </when> 37 </when>
34 </conditional> 38 </conditional>
35 </inputs> 39 </inputs>
36 <outputs> 40 <outputs>
74 chr_m.fasta is the reference file and the index chr_m.fasta.fai 78 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 79 these should be in the same directory, and chrM is from equCab2
76 --> 80 -->
77 <param name="index_source" value="cached" /> 81 <param name="index_source" value="cached" />
78 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> 82 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
83 <param name="index" value="chr_m" />
79 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /> 84 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
80 </test> 85 </test>
81 </tests> 86 </tests>
82 <help> 87 <help>
83 88