| Previous changeset 10:f867422772d6 (2019-10-17) Next changeset 12:e522022137f6 (2019-12-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642" |
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modified:
bcftools_consensus.xml |
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| diff -r f867422772d6 -r a87ae767b01d bcftools_consensus.xml --- a/bcftools_consensus.xml Thu Oct 17 02:49:33 2019 -0400 +++ b/bcftools_consensus.xml Wed Oct 23 19:30:14 2019 -0400 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2"> <description>Create consensus sequence by applying VCF variants to a reference fasta file</description> <macros> <token name="@EXECUTABLE@">consensus</token> @@ -7,6 +7,7 @@ </macros> <expand macro="requirements"> <expand macro="samtools_requirement"/> + <requirement type="package" version="5.0.1">gawk</requirement> </expand> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @@ -25,21 +26,27 @@ ${section.iupac_codes} #if $section.mask: - --mask "${section.mask}" + --mask '${section.mask}' #end if #if $section.select_haplotype: - --haplotype "${section.select_haplotype}" + --haplotype '${section.select_haplotype}' #end if @SAMPLE@ #if $chain: - --chain "$chain_file" + --chain '$chain_file' #end if ## Primary Input/Outputs ---output "$output_file" +#if str($rename) == "no" + --output '$output_file' +#end if @INPUT_FILE@ +#if str($rename) == "yes": + #set basename=$input_file.element_identifier + | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name="${basename}"} else {name=sprintf("%s-%d","${basename}",i);} print(gensub(/>[^ ]+( ?.*)/, ">" name "\\1", 1)); i=i+1;} else {print}}' > '$output_file' +#end if ]]> </command> <inputs> @@ -56,6 +63,7 @@ </param> </section> <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" /> + <param name="rename" type="boolean" truevalue="yes" falsevalue="no" label="Set output FASTA ID from name of VCF" /> </inputs> <outputs> <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/> @@ -96,6 +104,21 @@ </assert_contents> </output> </test> + <test> + <expand macro="test_using_reference" ref="consensus.fa" /> + <param name="input_file" ftype="vcf" value="consensus.vcf" /> + <param name="mask" ftype="tabular" value="consensus.tab" /> + <param name="chain" value="False" /> + <param name="rename" value="True" /> + <output name="output_file"> + <assert_contents> + <has_text text=">consensus.vcf" /> + </assert_contents> + <assert_contents> + <has_text text=">consensus.vcf-2" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ ===================================== @@ -108,6 +131,12 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ @BCFTOOLS_WIKI@ + +The option to set the new consensus' FASTA ID from the name of the VCF is provided by post-processing +the bcftools consensus output. It is primarily intended for use when the VCF is coming from a list +collection where the elements of the list are named meaningfully (e.g. named after sample names). This +is useful when consensus sequences are being prepared for, for example, feeding a multiple sequence +alignment to a phylogeny program. ]]> </help> <expand macro="citations" /> |