Mercurial > repos > iuc > gemini
annotate gemini_load.xml @ 19:27ce3de83007 draft
Deleted selected files
| author | iuc |
|---|---|
| date | Fri, 16 Oct 2015 13:55:09 -0400 |
| parents | 65f742e605ec |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> |
| 2 | 2 <description>Loading a VCF file into GEMINI</description> |
| 0 | 3 <macros> |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">load</token> | |
| 6 </macros> | |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
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changeset
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7 <expand macro="requirements" /> |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
8 <expand macro="stdio" /> |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
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9 <expand macro="version_command" /> |
| 0 | 10 <command> |
| 11 <![CDATA[ | |
| 15 | 12 ln -s "${ infile }" input.vcf && |
| 13 | |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
14 gemini |
| 5 | 15 --annotation-dir ${annotation_databases.fields.path} |
| 4 | 16 @BINARY@ |
| 15 | 17 -v input.vcf |
| 11 | 18 #if str( $annotation_type ) != "None": |
| 19 -t $annotation_type | |
| 20 #end if | |
| 0 | 21 |
| 22 #if $ped: | |
| 23 -p $ped | |
| 24 #end if | |
| 25 | |
| 26 $skip_gerp_bp | |
| 27 $skip_cadd | |
| 28 $skip_gene_tables | |
| 29 $no_load_genotypes | |
| 30 $no_genotypes | |
| 31 $passonly | |
| 32 --cores \${GALAXY_SLOTS:-4} | |
| 33 | |
| 34 "${ outfile }" | |
| 35 ]]> | |
| 36 </command> | |
| 37 <inputs> | |
| 14 | 38 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported."> |
| 39 <options> | |
| 40 <filter type="add_value" value="hg19" /> | |
| 41 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" /> | |
| 42 <filter type="add_value" value="hg_g1k_v37" /> | |
| 43 </options> | |
| 44 </param> | |
| 0 | 45 |
| 46 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)"> | |
| 11 | 47 <option value="None">None (not recommended)</option> |
| 48 <option value="snpEff" selected="True">snpEff annotated VCF file</option> | |
| 0 | 49 <option value="VEP">VEP annotated VCF file</option> |
| 50 </param> | |
| 51 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" /> | |
| 4 | 52 <expand macro="annotation_dir" /> |
| 0 | 53 |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
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54 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False" |
| 0 | 55 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/> |
| 56 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
57 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False" |
| 0 | 58 label="Do not load CADD scores" help="(--skip-cadd)"/> |
| 59 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
60 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False" |
| 0 | 61 label="Do not load gene tables" help="(--skip-gene-tables)"/> |
| 62 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
63 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" |
| 0 | 64 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/> |
| 65 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
66 <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" |
| 0 | 67 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/> |
| 68 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
15
diff
changeset
|
69 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False" |
| 0 | 70 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/> |
| 71 | |
| 72 </inputs> | |
| 73 <outputs> | |
| 11 | 74 <data name="outfile" format="gemini.sqlite" /> |
| 0 | 75 </outputs> |
| 76 <tests> | |
| 77 <test> | |
| 78 </test> | |
| 79 </tests> | |
| 80 <help> | |
| 81 **What it does** | |
| 82 | |
| 83 Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework. | |
| 84 We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff. | |
| 85 | |
| 86 http://gemini.readthedocs.org/en/latest/content/loading.html | |
| 87 | |
| 88 @CITATION@ | |
| 89 </help> | |
| 90 <expand macro="citations"/> | |
| 91 </tool> |