Mercurial > repos > jjohnson > shear
annotate shear_sv.xml @ 3:630532975fa9
Fix more typos
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 08 Jul 2013 01:10:38 -0500 |
| parents | 239e200ae99f |
| children | a82400332451 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.1"> | |
| 3 <description>find SVs and estimate the heterogeneity levels from a BAM</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="0.1.2">shear</requirement> | |
| 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 --> | |
| 3 | 14 <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar sv -p $prefix |
| 0 | 15 -b $bamfile |
| 16 #if $genomeSource.refGenomeSource == 'indexed': | |
| 17 -f $genomeSource.ref_fastas.fields.path | |
| 18 -i $genomeSource.bwa_indices.fields.path | |
| 3 | 19 -t $genomeSource.twobit_indices.fields.path |
| 0 | 20 #else: |
| 21 -f $genomeSource.ref_fasta | |
| 22 -i $genomeSource.bwa_index | |
| 23 -t $genomeSource.twobit | |
| 24 #end if | |
| 25 </command> | |
| 26 <inputs> | |
| 27 <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/> | |
| 28 <!-- reference data --> | |
| 29 <conditional name="genomeSource"> | |
| 30 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?"> | |
| 31 <option value="indexed" selected="true">Use a cached reference genome</option> | |
|
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32 <!-- |
| 0 | 33 <option value="history">Use one from the history</option> |
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parents:
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34 --> |
| 0 | 35 </param> |
| 36 <when value="indexed"> | |
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parents:
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diff
changeset
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37 <param name="ref_fastas" type="select" label="Select a reference genome fasta"> |
| 0 | 38 <options from_data_table="all_fasta"> |
| 39 <filter type="sort_by" column="2" /> | |
| 40 <validator type="no_options" message="No reference fasta files are available" /> | |
| 41 </options> | |
| 42 </param> | |
|
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a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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43 <param name="twobit_indices" type="select" label="Select the reference genome 2bit"> |
| 0 | 44 <options from_data_table="twobit"> |
| 45 <filter type="sort_by" column="0" /> | |
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a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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46 <!-- |
| 0 | 47 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" /> |
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a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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48 --> |
| 0 | 49 <validator type="no_options" message="No indexes are available" /> |
| 50 </options> | |
| 51 </param> | |
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1
a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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52 <param name="bwa_indices" type="select" label="Select the reference genome bwa indices"> |
| 0 | 53 <options from_data_table="bwa_indexes"> |
| 54 <filter type="sort_by" column="2" /> | |
|
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a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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55 <!-- |
| 0 | 56 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" /> |
|
1
a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
57 --> |
| 0 | 58 <validator type="no_options" message="No indexes are available" /> |
| 59 </options> | |
| 60 </param> | |
| 61 </when> | |
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1
a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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62 <!-- |
| 0 | 63 <when value="history"> |
| 64 <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> | |
| 65 <param name="twobit" type="data" format="twobit" metadata_name="dbkey" label="Select a reference from history" /> | |
| 66 <param name="bwa_index" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> | |
| 67 </when> | |
|
1
a718ecb27e02
Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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68 --> |
| 0 | 69 </conditional> |
| 70 <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/> | |
| 71 </inputs> | |
| 72 <stdio> | |
| 73 <exit_code range="1:" level="fatal" description="Error" /> | |
| 74 </stdio> | |
| 75 <outputs> | |
| 76 <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: shear_sv.sdi" from_work_dir="shear_sv.sdi" /> | |
| 77 <data format="txt" name="report" label="${tool.name} on ${on_string}: shear_sv.report" from_work_dir="shear_sv.report"/> | |
| 78 </outputs> | |
| 79 <tests> | |
| 80 <test> | |
| 81 <param name="bamfile" ftype="bam" value="simulated-data.bam"/> | |
| 82 <param name="refGenomeSource" value="history"/> | |
| 83 <param name="ref_fasta" ftype="fasta" value="syn.fa"/> | |
| 84 <param name="bwa_index" ftype="" value="syn.fa"/> | |
| 85 <param name="twobit" ftype="twobit" value="syn.2bit"/> | |
| 86 <output name="shear.sdi" file="shear_sv.sdi"/> | |
| 87 <output name="report" file="shear_sv.report"/> | |
| 88 </test> | |
| 89 </tests> | |
| 90 <help> | |
| 91 SHEAR-SV will process a BAM alignment file to find SVs and estimate the | |
| 92 heterogeneity level of those SVs. It will output a *.report file reporing the | |
| 93 SVs and their heterogeneity levels, and it will output a *.sdi file that can be | |
| 94 used for SHEAR-Assemble to reconstruct the new genome. | |
| 95 </help> | |
| 96 </tool> |