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1 <?xml version="1.0"?>
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2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.1">
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3 <description>find SVs and estimate the heterogeneity levels from a BAM</description>
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4 <requirements>
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5 <requirement type="package" version="0.1.2">shear</requirement>
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6 <requirement type="package" version="0.1.18">samtools</requirement>
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7 <requirement type="package" version="0.6.2">bwa</requirement>
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8 <requirement type="package" version="1.0.1">crest</requirement>
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9 <requirement type="package" version="latest">kent</requirement>
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10 </requirements>
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11 <!--
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12 <version_command></version_command>
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13 -->
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14 <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar sv -r $prefix
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15 -b $bamfile
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16 #if $genomeSource.refGenomeSource == 'indexed':
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17 -f $genomeSource.ref_fastas.fields.path
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18 -i $genomeSource.bwa_indices.fields.path
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19 -t $genomeSource.twobit_indice.fields.paths
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20 #else:
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21 -f $genomeSource.ref_fasta
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22 -i $genomeSource.bwa_index
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23 -t $genomeSource.twobit
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/>
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28 <!-- reference data -->
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29 <conditional name="genomeSource">
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30 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
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31 <option value="indexed" selected="true">Use a cached reference genome</option>
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32 <option value="history">Use one from the history</option>
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33 </param>
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34 <when value="indexed">
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35 <param name="ref_fastas" type="select" label="Select a reference genome">
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36 <options from_data_table="all_fasta">
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37 <filter type="sort_by" column="2" />
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38 <validator type="no_options" message="No reference fasta files are available" />
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39 </options>
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40 </param>
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41 <param name="twobit_indices" type="select" label="Select a reference genome">
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42 <options from_data_table="twobit">
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43 <filter type="sort_by" column="0" />
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44 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
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45 <validator type="no_options" message="No indexes are available" />
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46 </options>
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47 </param>
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48 <param name="bwa_indices" type="select" label="Select a reference genome">
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49 <options from_data_table="bwa_indexes">
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50 <filter type="sort_by" column="2" />
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51 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
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52 <validator type="no_options" message="No indexes are available" />
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53 </options>
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54 </param>
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55 </when>
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56 <when value="history">
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57 <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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58 <param name="twobit" type="data" format="twobit" metadata_name="dbkey" label="Select a reference from history" />
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59 <param name="bwa_index" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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60 </when>
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61 </conditional>
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62 <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
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63 </inputs>
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64 <stdio>
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65 <exit_code range="1:" level="fatal" description="Error" />
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66 </stdio>
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67 <outputs>
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68 <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: shear_sv.sdi" from_work_dir="shear_sv.sdi" />
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69 <data format="txt" name="report" label="${tool.name} on ${on_string}: shear_sv.report" from_work_dir="shear_sv.report"/>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="bamfile" ftype="bam" value="simulated-data.bam"/>
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74 <param name="refGenomeSource" value="history"/>
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75 <param name="ref_fasta" ftype="fasta" value="syn.fa"/>
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76 <param name="bwa_index" ftype="" value="syn.fa"/>
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77 <param name="twobit" ftype="twobit" value="syn.2bit"/>
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78 <output name="shear.sdi" file="shear_sv.sdi"/>
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79 <output name="report" file="shear_sv.report"/>
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80 </test>
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81 </tests>
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82 <help>
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83 SHEAR-SV will process a BAM alignment file to find SVs and estimate the
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84 heterogeneity level of those SVs. It will output a *.report file reporing the
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85 SVs and their heterogeneity levels, and it will output a *.sdi file that can be
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86 used for SHEAR-Assemble to reconstruct the new genome.
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87 </help>
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88 </tool>
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