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
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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3">
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2 <description>converts SAM format to BAM format</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.18">samtools</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 sam_to_bam.py
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8 --input1=$source.input1
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9 #if $source.index_source == "history":
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10 --ref_file=$source.ref_file
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11 #else
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12 --index=${source.index.fields.path}
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13 #end if
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14 --output1=$output1
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15 </command>
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16 <inputs>
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17 <conditional name="source">
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18 <param name="index_source" type="select" label="Choose the source for the reference list">
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19 <option value="cached">Locally cached</option>
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20 <option value="history">History</option>
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21 </param>
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22 <when value="cached">
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23 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert">
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24 <validator type="unspecified_build" />
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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." />
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26 </param>
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27 <param name="index" type="select" label="Using reference genome">
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28 <options from_data_table="fasta_indexes">
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29 <filter type="data_meta" ref="input1" key="dbkey" column="1" />
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30 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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31 </options>
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32 </param>
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33 </when>
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34 <when value="history">
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35 <param name="input1" type="data" format="sam" label="SAM file to convert" />
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36 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
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42 <actions>
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43 <conditional name="source.index_source">
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44 <when value="cached">
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45 <action type="metadata" name="dbkey">
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46 <option type="from_param" name="source.input1" param_attribute="dbkey" />
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47 </action>
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48 </when>
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49 <when value="history">
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50 <action type="metadata" name="dbkey">
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51 <option type="from_param" name="source.ref_file" param_attribute="dbkey" />
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52 </action>
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53 </when>
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54 </conditional>
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55 </actions>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <!--
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61 Sam-to-Bam command:
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62 cp test-data/chr_m.fasta .
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63 samtools faidx chr_m.fasta
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64 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
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65 samtools sort unsorted.bam sam_to_bam_out1
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66 chr_m.fasta is the reference file (chrM from equCab2)
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67 -->
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68 <param name="index_source" value="history" />
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69 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
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70 <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
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71 <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
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72 </test>
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73 <test>
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74 <!--
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75 Sam-to-Bam command:
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76 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
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77 samtools sort unsorted.bam sam_to_bam_out2
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78 chr_m.fasta is the reference file and the index chr_m.fasta.fai
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79 these should be in the same directory, and chrM is from equCab2
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80 -->
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81 <param name="index_source" value="cached" />
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82 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
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83 <param name="index" value="chr_m" />
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84 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
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85 </test>
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86 </tests>
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87 <help>
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88
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89 **What it does**
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90
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91 This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.
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92
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93 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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94
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95 ------
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96
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97 **Citation**
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98
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
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100
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101 </help>
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102 </tool>