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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2">
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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 $source.index_source == "history":
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10 --dbkey=${ref_file.metadata.dbkey}
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11 --ref_file=$source.ref_file
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12 #else
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13 --dbkey=${input1.metadata.dbkey}
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14 #end if
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15 --output1=$output1
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16 --index_dir=${GALAXY_DATA_INDEX_DIR}
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17 </command>
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18 <inputs>
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19 <conditional name="source">
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20 <param name="index_source" type="select" label="Choose the source for the reference list">
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21 <option value="cached">Locally cached</option>
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22 <option value="history">History</option>
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23 </param>
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24 <when value="cached">
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25 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
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26 <validator type="unspecified_build" />
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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" />
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28 </param>
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29 </when>
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30 <when value="history">
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31 <param name="input1" type="data" format="sam" label="Convert SAM file" />
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32 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <outputs>
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37 <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
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38 <actions>
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39 <conditional name="source.index_source">
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40 <when value="cached">
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41 <action type="metadata" name="dbkey">
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42 <option type="from_param" name="source.input1" param_attribute="dbkey" />
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43 </action>
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44 </when>
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45 <when value="history">
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46 <action type="metadata" name="dbkey">
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47 <option type="from_param" name="source.ref_file" param_attribute="dbkey" />
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48 </action>
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49 </when>
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50 </conditional>
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51 </actions>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <!--
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57 Sam-to-Bam command:
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58 cp test-data/chr_m.fasta .
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59 samtools faidx chr_m.fasta
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60 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
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61 samtools sort unsorted.bam sam_to_bam_out1
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62 chr_m.fasta is the reference file (chrM from equCab2)
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63 -->
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64 <param name="index_source" value="history" />
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65 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
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66 <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
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67 <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
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68 </test>
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69 <test>
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70 <!--
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71 Sam-to-Bam command:
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72 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
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73 samtools sort unsorted.bam sam_to_bam_out2
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74 chr_m.fasta is the reference file and the index chr_m.fasta.fai
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75 these should be in the same directory, and chrM is from equCab2
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76 -->
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77 <param name="index_source" value="cached" />
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78 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
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79 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
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80 </test>
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81 </tests>
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82 <help>
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83
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84 **What it does**
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85
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86 This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.
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87
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88 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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89
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90 ------
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91
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92 **Citation**
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93
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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>`_
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95
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96 </help>
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97 </tool>
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