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annotate vcfcheck.xml @ 2:265e5230925c draft

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author devteam
date Thu, 15 Sep 2016 16:03:14 -0400
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children 713575be4f77
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265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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1 <tool id="vcfcheck" name="VCFcheck:" version="@WRAPPER_VERSION@.0">
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2 <description>Verify that the reference allele matches the reference genome</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"></expand>
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7 <stdio>
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8 <regex match="index file" source="stderr" level="warning"/>
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9 </stdio>
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10 <command>
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11 #set $reference_fasta_filename = "localref.fa"
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12 #if str( $reference_source.reference_source_selector ) == "history":
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 #else:
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15 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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16 #end if
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17 vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 <inputs>
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19 <conditional name="reference_source">
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20 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <option value="cached">Locally cached</option>
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22 <option value="history">History</option>
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23 </param>
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24 <when value="cached">
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25 <param name="ref_file" type="select" label="Select reference genome">
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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26 <options from_data_table="fasta_indexes">
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27 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </options>
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29 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </param>
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31 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
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32 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
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33 <validator type="unspecified_build" />
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34 <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." />
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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35 -->
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36 </param>
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37 </when>
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38 <when value="history"> <!-- FIX ME!!!! -->
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39 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
265e5230925c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
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41 </when>
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42 </conditional>
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43 <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
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44 <option value="-x">Exculde failures (-x option)</option>
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45 <option value="-k">Keep failures (-k option)</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data format="vcf" name="out_file1" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="reference_source_selector" value="history" />
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54 <param name="failure_selection" value="-x" />
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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="vcfcheck-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 Verifies that the VCF REF field matches the reference as described.
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63
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64 The options are::
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65
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66 -x, --exclude-failures If a record fails, don't print it. Otherwise do.
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67 -k, --keep-failures Print if the record fails, otherwise not.
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68
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69 ----
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71 Vcfcheck @IS_PART_OF_VCFLIB@
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72 </help>
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73 <expand macro="citations" />
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74 </tool>