| Previous changeset 0:639b3a5bb415 (2018-05-30) Next changeset 2:f1cb13497323 (2018-06-05) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9 |
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modified:
macros.xml nanopolish_variants.xml |
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added:
test-data/all_fasta.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 639b3a5bb415 -r 1ebed8b65752 macros.xml --- a/macros.xml Wed May 30 11:56:35 2018 -0400 +++ b/macros.xml Tue Jun 05 17:58:46 2018 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.9.0">nanopolish</requirement> + <requirement type="package" version="0.9.2">nanopolish</requirement> <yield/> </requirements> </xml> @@ -33,4 +33,4 @@ <yield /> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r 639b3a5bb415 -r 1ebed8b65752 nanopolish_variants.xml --- a/nanopolish_variants.xml Wed May 30 11:56:35 2018 -0400 +++ b/nanopolish_variants.xml Tue Jun 05 17:58:46 2018 -0400 |
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| @@ -17,7 +17,11 @@ nanopolish index -d fast5_files/ reads.fasta && ln -s '$b' reads.bam && ln -s '${b.metadata.bam_index}' reads.bam.bai && - ln -s '$g' genome.fa && + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' genome.fa && + #else: + ln -f -s '$reference_source.ref_file.fields.path' genome.fa && + #end if nanopolish variants -r reads.fasta @@ -38,6 +42,10 @@ -d $min_candidate_depth -x $max_haplotypes --max-rounds $max_rounds + --threads "\${GALAXY_SLOTS:-4}" + #if str($min_flanking_sequence): + --min-flanking-sequence $min_flanking_sequence + #end if #if $ploidy != -1: --ploidy $ploidy #end if @@ -64,8 +72,6 @@ #if $adv.input_models_fofn: --models-fofn '$input_models_fofn' #end if - - ]]></command> <inputs> @@ -75,7 +81,22 @@ <!-- variants consensus inputs --> <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> - <param type="data" argument="-g" format="fasta" label="The reference genome"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> <section name="adv" title="Optional data inputs"> <!-- optional inputs --> @@ -98,6 +119,7 @@ <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/> <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/> <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/> + <param name="min_flanking_sequence" type="integer" optional="true" value="" label="Distance from alignment end to calculate variants" help="(--min-flanking-sequence)"/> <!-- optional flags --> <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" /> @@ -117,36 +139,41 @@ </outputs> <tests> <test> - <!-- index test --> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> - - <!-- variants consensus test --> <param name="b" value="reads.sorted.bam" /> - <param name="g" value="draft.fa" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-202000" /> - <output name="output_polished" file="polished.fa" /> <output name="output_variants" file="variants.vcf"/> </test> <test> - <!-- index test --> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> - - <!-- variants consensus test --> <param name="b" value="reads.sorted.bam" /> - <param name="g" value="draft.fa" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-202000" /> <param name="ploidy" value="2" /> <param name="snps" value="true" /> <param name="faster" value="true" /> <param name="all_bases" value="true" /> <param name="consensus" value="false" /> + <param name="min_flanking_sequence" value="30" /> <output name="output_polished" file="t2-polished.fa" /> <output name="output_variants" file="t2-variants.vcf"/> </test> - + <test> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + <param name="b" value="reads.sorted.bam" /> + <param name="reference_source_selector" value="cached" /> + <param name="ref_file" value="draft"/> + <param name="w" value="tig00000001:200000-202000" /> + <output name="output_polished" file="polished.fa" /> + <output name="output_variants" file="variants.vcf"/> + </test> </tests> <help><![CDATA[ |
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| diff -r 639b3a5bb415 -r 1ebed8b65752 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Jun 05 17:58:46 2018 -0400 |
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| @@ -0,0 +1,1 @@ +draft draft draft ${__HERE__}/draft.fa \ No newline at end of file |
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| diff -r 639b3a5bb415 -r 1ebed8b65752 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 05 17:58:46 2018 -0400 |
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| @@ -0,0 +1,9 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> + |
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| diff -r 639b3a5bb415 -r 1ebed8b65752 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 05 17:58:46 2018 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |