Mercurial > repos > devteam > vcfgeno2haplo
comparison vcfgeno2haplo.xml @ 4:a3dea556218d draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 36e9065027cc7bf721e9d203208477ee88906c57"
author | iuc |
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date | Thu, 23 Jan 2020 08:08:59 -0500 |
parents | b890055e07bd |
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3:b890055e07bd | 4:a3dea556218d |
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3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command> | 8 <command><![CDATA[ |
9 #set $reference_fasta_filename = "localref.fa" | 9 #set $reference_fasta_filename = "localref.fa" |
10 #if str( $reference_source.reference_source_selector ) == "history": | 10 #if str( $reference_source.reference_source_selector ) == "history": |
11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | 11 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && |
12 #else: | 12 #else: |
13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | 13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
14 #end if | 14 #end if |
15 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command> | 15 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}" |
16 ]]></command> | |
16 <inputs> | 17 <inputs> |
17 <conditional name="reference_source"> | 18 <conditional name="reference_source"> |
18 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | 19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
19 <option value="cached">Locally cached</option> | 20 <option value="cached">Locally cached</option> |
20 <option value="history">History</option> | 21 <option value="history">History</option> |
22 <when value="cached"> | 23 <when value="cached"> |
23 <param name="ref_file" type="select" label="Select reference genome"> | 24 <param name="ref_file" type="select" label="Select reference genome"> |
24 <options from_data_table="fasta_indexes"> | 25 <options from_data_table="fasta_indexes"> |
25 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> | 26 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> |
26 </options> | 27 </options> |
27 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | 28 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
28 </param> | 29 </param> |
29 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset"> | 30 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset"> |
30 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future | 31 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future |
31 <validator type="unspecified_build" /> | 32 <validator type="unspecified_build" /> |
32 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> | 33 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> |
33 --> | 34 --> |
34 </param> | 35 </param> |
35 </when> | 36 </when> |
36 <when value="history"> <!-- FIX ME!!!! --> | 37 <when value="history"> <!-- FIX ME!!!! --> |
37 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | 38 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
38 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" /> | 39 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" /> |
39 </when> | 40 </when> |
40 </conditional> | 41 </conditional> |
41 <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" /> | 42 <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" /> |
42 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" /> | 43 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" /> |
43 <!-- <option value=" ">Output entire haplotype</option> | 44 <!-- <option value=" ">Output entire haplotype</option> |
44 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by ":")</option> | 45 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by ":")</option> |
45 </param> --> | 46 </param> --> |
46 </inputs> | 47 </inputs> |
47 <outputs> | 48 <outputs> |
48 <data format="vcf" name="out_file1" /> | 49 <data format="vcf" name="out_file1" /> |
54 <param name="window_size" value="5000" /> | 55 <param name="window_size" value="5000" /> |
55 <param name="input_vcf" value="vcflib-phix.vcf"/> | 56 <param name="input_vcf" value="vcflib-phix.vcf"/> |
56 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | 57 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
57 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/> | 58 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/> |
58 </test> | 59 </test> |
59 </tests> | 60 </tests> |
60 <help> | 61 <help> |
61 | 62 |
62 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input. | 63 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input. |
63 | 64 |
64 The options are:: | 65 The options are:: |