Mercurial > repos > jjohnson > shear
annotate shear_assemble.xml @ 8:8fac6c7d32fd
Copy reference fasta for shear sv to avoid GATK issue with symlinks
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 22 Oct 2013 09:44:32 -0500 |
| parents | 8180f6b0249b |
| children | 2620f7984418 |
| rev | line source |
|---|---|
| 7 | 1 <tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.3"> |
| 0 | 2 <description>create a personal genome from sdi</description> |
| 3 <requirements> | |
| 7 | 4 <requirement type="package" version="0.2.4">shear</requirement> |
| 0 | 5 </requirements> |
| 6 <!-- | |
| 7 <version_command></version_command> | |
| 8 --> | |
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Use shear_wrapper.py to generate reference indexes when needed
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9 <command interpreter="python"> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
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10 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command assemble |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
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parents:
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11 -p $prefix |
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Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
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12 -s $sdi_file |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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13 #if $genomeSource.refGenomeSource == 'indexed': |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
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14 -f $genomeSource.ref_fastas.fields.path |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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15 #else: |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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16 -f $genomeSource.ref_fasta |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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17 #end if |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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18 -o $output_fasta |
| 0 | 19 </command> |
| 20 <inputs> | |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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21 <param name="prefix" type="text" value="shear_assemble" label="Prefix for all generated files"> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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diff
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22 <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
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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23 </param> |
| 0 | 24 <param name="sdi_file" type="data" format="shear.sdi" label="SDI file produced by SHEAR's 'sv' command containing the SVs to use to create the new genomic sequence."/> |
| 25 <!-- reference data --> | |
| 26 <conditional name="genomeSource"> | |
| 27 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?"> | |
| 28 <option value="indexed">Use a cached reference genome</option> | |
| 29 <option value="history">Use one from the history</option> | |
| 30 </param> | |
| 31 <when value="indexed"> | |
| 32 <param name="ref_fastas" type="select" label="Select a reference genome"> | |
| 33 <options from_data_table="all_fasta"> | |
| 34 <filter type="sort_by" column="2" /> | |
| 35 <validator type="no_options" message="No reference fasta files are available" /> | |
| 36 </options> | |
| 37 </param> | |
| 38 </when> | |
| 39 <when value="history"> | |
| 40 <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> | |
| 41 </when> | |
| 42 </conditional> | |
| 43 </inputs> | |
| 44 <stdio> | |
| 45 <exit_code range="1:" level="fatal" description="Error" /> | |
| 46 </stdio> | |
| 47 <outputs> | |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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48 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: ${prefix}.fa" /> |
| 0 | 49 </outputs> |
| 50 <tests> | |
| 51 <test> | |
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Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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52 <param name="prefix" value="shear_assembly" /> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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53 <param name="sdi_file" value="shear_sv.sdi" ftype="shear.sdi" /> |
| 0 | 54 <param name="refGenomeSource" value="history"/> |
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a82400332451
Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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55 <param name="ref_fasta" value="syn.fa" ftype="fasta" /> |
| 0 | 56 <output name="output_fasta" file="simulated-data.fa"/> |
| 57 </test> | |
| 58 </tests> | |
| 59 <help> | |
| 60 SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome. | |
| 61 </help> | |
| 62 </tool> |