Mercurial > repos > bgruening > nanopolish_methylation
changeset 1:709490665bad draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
| author | bgruening |
|---|---|
| date | Tue, 05 Jun 2018 17:56:11 -0400 |
| parents | f9dadc362197 |
| children | 07cf146e8964 |
| files | macros.xml nanopolish_methylation.xml test-data/all_fasta.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 5 files changed, 59 insertions(+), 11 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Wed May 30 11:55:55 2018 -0400 +++ b/macros.xml Tue Jun 05 17:56:11 2018 -0400 @@ -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>
--- a/nanopolish_methylation.xml Wed May 30 11:55:55 2018 -0400 +++ b/nanopolish_methylation.xml Tue Jun 05 17:56:11 2018 -0400 @@ -17,12 +17,20 @@ 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 '$reference_source.ref_file.fields.path' genome.fa && + #end if nanopolish call-methylation -r reads.fasta -b reads.bam -g genome.fa + #if str($batchsize): + -K $batchsize + #end if + --threads "\${GALAXY_SLOTS:-4}" #if $w and str($w).strip(): -w "${w}" #end if @@ -35,10 +43,25 @@ <!-- 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> <param argument="-w" type="text" optional="true" label="find variants in window of region chromsome:start-end" /> + <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/> </inputs> @@ -48,18 +71,26 @@ </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" /> - + <param name="batchsize" value="512" /> <output name="output_methylation_calls" file="methylation_calls.tsv" /> </test> - </tests> + <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="reference_source_selector" value="cached" /> + <param name="ref_file" value="draft"/> + <param name="b" value="reads.sorted.bam" /> + <param name="w" value="tig00000001:200000-202000" /> + <param name="batchsize" value="512" /> + <output name="output_methylation_calls" file="methylation_calls.tsv" /> + </test> + </tests> <help><![CDATA[ Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa Classify nucleotides as methylated or not.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Jun 05 17:56:11 2018 -0400 @@ -0,0 +1,1 @@ +draft draft draft ${__HERE__}/draft.fa \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 05 17:56:11 2018 -0400 @@ -0,0 +1,9 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 05 17:56:11 2018 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables>