Mercurial > repos > devteam > vcfgeno2haplo

annotate vcfgeno2haplo.xml @ 3:25d297ce9ccb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:14:25 -0400
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children 00f74c1efa2d
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25d297ce9ccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="@WRAPPER_VERSION@+galaxy0">
2
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2 <description>Convert genotype-based phased alleles into haplotype alleles</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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8 <command>
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9 #set $reference_fasta_filename = "localref.fa"
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10 #if str( $reference_source.reference_source_selector ) == "history":
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11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
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12 #else:
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13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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14 #end if
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15 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
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16 <inputs>
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17 <conditional name="reference_source">
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18 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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19 <option value="cached">Locally cached</option>
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20 <option value="history">History</option>
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21 </param>
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22 <when value="cached">
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23 <param name="ref_file" type="select" label="Select reference genome">
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24 <options from_data_table="fasta_indexes">
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25 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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26 </options>
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27 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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28 </param>
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29 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
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30 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
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31 <validator type="unspecified_build" />
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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." />
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33 -->
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34 </param>
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35 </when>
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36 <when value="history"> <!-- FIX ME!!!! -->
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37 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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38 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
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39 </when>
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40 </conditional>
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41 <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
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42 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
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43 <!-- <option value=" ">Output entire haplotype</option>
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44 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
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45 </param> -->
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46 </inputs>
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47 <outputs>
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48 <data format="vcf" name="out_file1" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="reference_source_selector" value="history" />
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53 <param name="output_option" value="true" />
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54 <param name="window_size" value="5000" />
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55 <param name="input_vcf" value="vcflib-phix.vcf"/>
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56 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
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57 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
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58 </test>
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59 </tests>
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60 <help>
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61
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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.
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63
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64 The options are::
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65
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66 -w, --window-size N Merge variants at most this many bp apart (default 30)
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67 -o, --only-variants Don't output the entire haplotype, just concatenate
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68 REF/ALT strings (delimited by ":")
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69
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70 ----
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71
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72 Vcfgeno2haplo @IS_PART_OF_VCFLIB@
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73 </help>
d731d6f785b5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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74 <expand macro="citations" />
d731d6f785b5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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75 </tool>