Mercurial > repos > jjohnson > shear
annotate shear_sv.xml @ 5:aaaa5a071ff0
Update to SHEAR v 0.2.3
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 17 Oct 2013 08:01:38 -0500 |
| parents | a82400332451 |
| children | 0158f7356ffd |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 5 | 2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.2"> |
| 0 | 3 <description>find SVs and estimate the heterogeneity levels from a BAM</description> |
| 4 <requirements> | |
| 5 | 5 <requirement type="package" version="0.2.3">shear</requirement> |
| 0 | 6 <requirement type="package" version="0.1.18">samtools</requirement> |
| 7 <requirement type="package" version="0.6.2">bwa</requirement> | |
| 8 <requirement type="package" version="1.0.1">crest</requirement> | |
| 9 <requirement type="package" version="latest">kent</requirement> | |
| 10 </requirements> | |
| 11 <!-- | |
| 12 <version_command></version_command> | |
| 13 --> | |
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Use shear_wrapper.py to generate reference indexes when needed
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14 <command interpreter="python"> |
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15 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command sv |
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16 -p $prefix |
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17 -b $bamfile |
| 0 | 18 #if $genomeSource.refGenomeSource == 'indexed': |
| 19 -f $genomeSource.ref_fastas.fields.path | |
| 20 -i $genomeSource.bwa_indices.fields.path | |
| 3 | 21 -t $genomeSource.twobit_indices.fields.path |
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22 #elif $genomeSource.refGenomeSource == 'svidx': |
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a82400332451
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parents:
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23 -f $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa |
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a82400332451
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Jim Johnson <jj@umn.edu>
parents:
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24 -i $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa |
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a82400332451
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parents:
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25 -t $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.2bit |
| 0 | 26 #else: |
| 27 -f $genomeSource.ref_fasta | |
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28 #if $genomeSource.save_svidx: |
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29 -D $sv_idx.extra_files_path |
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30 #end if |
| 0 | 31 #end if |
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32 --report $report |
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33 --sdi $sdi |
| 0 | 34 </command> |
| 35 <inputs> | |
| 36 <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/> | |
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parents:
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37 <param name="prefix" type="text" value="shear_sv" label="Prefix for all generated files"> |
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parents:
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38 <validator type="regex" message="Prefix should start with a letter and contain only letter, digit, and '_' or '-' characters">[a-zA-Z0-9][_a-zA-Z0-9-]*</validator> |
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a82400332451
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parents:
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39 </param> |
| 0 | 40 <!-- reference data --> |
| 41 <conditional name="genomeSource"> | |
| 42 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?"> | |
| 43 <option value="indexed" selected="true">Use a cached reference genome</option> | |
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44 <option value="history">Use fasta from the history</option> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
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45 <option value="svidx">Use SHEAR sv index from the history</option> |
| 0 | 46 </param> |
| 47 <when value="indexed"> | |
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48 <param name="ref_fastas" type="select" label="Select a reference genome fasta"> |
| 0 | 49 <options from_data_table="all_fasta"> |
| 50 <filter type="sort_by" column="2" /> | |
| 51 <validator type="no_options" message="No reference fasta files are available" /> | |
| 52 </options> | |
| 53 </param> | |
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54 <param name="twobit_indices" type="select" label="Select the reference genome 2bit"> |
| 0 | 55 <options from_data_table="twobit"> |
| 56 <filter type="sort_by" column="0" /> | |
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57 <!-- |
| 0 | 58 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" /> |
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59 --> |
| 0 | 60 <validator type="no_options" message="No indexes are available" /> |
| 61 </options> | |
| 62 </param> | |
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63 <param name="bwa_indices" type="select" label="Select the reference genome bwa indices"> |
| 0 | 64 <options from_data_table="bwa_indexes"> |
| 65 <filter type="sort_by" column="2" /> | |
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66 <!-- |
| 0 | 67 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" /> |
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68 --> |
| 0 | 69 <validator type="no_options" message="No indexes are available" /> |
| 70 </options> | |
| 71 </param> | |
| 72 </when> | |
| 73 <when value="history"> | |
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Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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74 <param name="ref_fasta" type="data" format="fasta" label="Select a reference from history" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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75 <param name="save_svidx" type="boolean" truevalue="yes" falsevalue="no" label="Save sv generated reference indexes"/> |
| 0 | 76 </when> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
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77 <when value="svidx"> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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78 <param name="svidx" type="data" format="shear.svidx" label="Select a reference from history" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
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79 </when> |
| 0 | 80 </conditional> |
| 81 </inputs> | |
| 82 <stdio> | |
| 83 <exit_code range="1:" level="fatal" description="Error" /> | |
| 84 </stdio> | |
| 85 <outputs> | |
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parents:
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86 <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: ${prefix}.sdi" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
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87 <data format="txt" name="report" label="${tool.name} on ${on_string}: ${prefix}.report" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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88 <data format="shear.svidx" name="sv_idx" label="${tool.name} on ${on_string}: ${prefix}.svidx"> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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89 <filter>genomeSource['refGenomeSource'] == 'history' and genomeSource['save_svidx'] == True</filter> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
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90 </data> |
| 0 | 91 </outputs> |
| 92 <tests> | |
| 93 <test> | |
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parents:
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94 <param name="prefix" value="shear_test" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
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95 <param name="bamfile" value="simulated-data.bam" ftype="bam" /> |
| 0 | 96 <param name="refGenomeSource" value="history"/> |
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parents:
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97 <param name="ref_fasta" value="syn.fa" ftype="fasta" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
3
diff
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98 <output name="sdi" file="shear_sv.sdi"/> |
| 0 | 99 <output name="report" file="shear_sv.report"/> |
| 100 </test> | |
| 101 </tests> | |
| 102 <help> | |
| 103 SHEAR-SV will process a BAM alignment file to find SVs and estimate the | |
| 104 heterogeneity level of those SVs. It will output a *.report file reporing the | |
| 105 SVs and their heterogeneity levels, and it will output a *.sdi file that can be | |
| 106 used for SHEAR-Assemble to reconstruct the new genome. | |
| 107 </help> | |
| 108 </tool> |