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annotate sam_to_bam.xml @ 2:5a5f92086188 draft

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author devteam
date Tue, 13 Oct 2015 12:53:53 -0400
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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
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2 <description>convert SAM to BAM</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command>
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10 <![CDATA[
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11 #if $source.index_source == "history":
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12 ln -s $source.ref_file input.fa &&
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13 samtools faidx input.fa &&
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14 #else
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15 ln -s ${source.index.fields.path} input.fa &&
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16 ln -s ${source.index.fields.path}.fai input.fa.fai &&
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17 #end if
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18 samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
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19 ]]>
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20 </command>
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21 <inputs>
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22 <conditional name="source">
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23 <param label="Choose the source for the reference genome" name="index_source" type="select">
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24 <option value="cached">Use a built-in genome</option>
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25 <option value="history">Use a genome from the history</option>
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26 </param>
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27 <when value="cached">
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28 <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data">
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29 <validator type="unspecified_build" />
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30 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
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31 </param>
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32 <param label="Using reference genome" name="index" type="select">
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33 <options from_data_table="fasta_indexes">
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34 <filter column="1" key="dbkey" ref="input1" type="data_meta" />
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35 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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36 </options>
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37 </param>
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38 </when>
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39 <when value="history">
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40 <param format="sam" label="SAM file to convert" name="input1" type="data" />
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41 <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" />
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1">
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47 <actions>
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48 <conditional name="source.index_source">
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49 <when value="cached">
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50 <action name="dbkey" type="metadata">
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51 <option name="source.input1" param_attribute="dbkey" type="from_param" />
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52 </action>
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53 </when>
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54 <when value="history">
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55 <action name="dbkey" type="metadata">
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56 <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
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57 </action>
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58 </when>
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59 </conditional>
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60 </actions>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="index_source" value="history" />
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66 <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
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67 <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
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68 <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
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69 </test>
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70 <test>
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71 <param name="index_source" value="history" />
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72 <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
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73 <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
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74 <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
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75 </test>
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76 </tests>
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77 <help>
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78 <![CDATA[
0
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79 **What it does**
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80
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81 Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands::
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82
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83 samtools sort -O bam -o sorted_input.bam [INPUT SAM]
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84 samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam
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85
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86 ]]>
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87 </help>
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88 <expand macro="citations"></expand>
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89 </tool>