| Previous changeset 7:a3afc5f0a96c (2021-07-30) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4 |
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modified:
macros.xml nanopolish_variants.xml |
| b |
| diff -r a3afc5f0a96c -r bec636361cfd macros.xml --- a/macros.xml Fri Jul 30 06:29:50 2021 +0000 +++ b/macros.xml Thu Nov 30 17:57:59 2023 +0000 |
| [ |
| @@ -1,5 +1,8 @@ <macros> - <token name="@VERSION@">0.13.2</token> + <token name="@VERSION@">0.14.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">nanopolish</requirement> @@ -19,6 +22,52 @@ <output name="output_index_readdb" file="reads.fasta.index.readdb" /> --> + + <token name="@PREPROCESS_INPUTS@"><![CDATA[ + ln -s '$input_merged' reads.fasta && + + mkdir fast5_files && + #if $input_reads_raw.extension == 'fast5': + ln -s '$input_reads_raw' fast5_files/read1.fast5 && + + #else if $input_reads_raw.extension == 'fast5.tar': + ln -s '$input_reads_raw' fast5_files.tar && + tar -xf fast5_files.tar -C fast5_files && + + #else if $input_reads_raw.extension == 'fast5.tar.bz2': + ln -s '$input_reads_raw' fast5_files.tar.bz2 && + tar -xjf fast5_files.tar.bz2 -C fast5_files && + + #else if $input_reads_raw.extension == 'fast5.tar.xz': + ln -s '$input_reads_raw' fast5_files.tar.xz && + tar -xf fast5_files.tar.xz -C fast5_files && + + #else if $input_reads_raw.extension == 'fast5.tar.gz': + ln -s '$input_reads_raw' fast5_files.tar.gz && + tar -xzf fast5_files.tar.gz -C fast5_files && + + #else: + echo 'Unsupported fast5 input type' && + exit 1 && + + #end if + + nanopolish index + -d fast5_files/ + #if $adv.input_seq_summary: + -s '$adv.input_seq_summary' + #end if + reads.fasta && + + ln -s '$b' reads.bam && + ln -s '${b.metadata.bam_index}' reads.bam.bai && + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' genome.fa && + #else: + ln -f -s '$reference_source.ref_file.fields.path' genome.fa && + #end if + ]]></token> + <xml name="citations"> <citations> <citation type="doi">10.1038/nmeth.3444</citation> |
| b |
| diff -r a3afc5f0a96c -r bec636361cfd nanopolish_variants.xml --- a/nanopolish_variants.xml Fri Jul 30 06:29:50 2021 +0000 +++ b/nanopolish_variants.xml Thu Nov 30 17:57:59 2023 +0000 |
| [ |
| @@ -1,43 +1,11 @@ -<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy0"> +<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$input_merged' reads.fasta && - - #if $input_reads_raw.extension == 'fast5': - mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && - - #else if $input_reads_raw.extension == 'fast5.tar': - ln -s '$input_reads_raw' fast5_files.tar && - mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files && - - #else if $input_reads_raw.extension == 'fast5.tar.bz2': - ln -s '$input_reads_raw' fast5_files.tar.bz2 && - mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files && - - #else: - ln -s '$input_reads_raw' fast5_files.tar.gz && - mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && - - #end if - - nanopolish index - -d fast5_files/ - #if $adv.input_seq_summary: - -s '$adv.input_seq_summary' - #end if - reads.fasta && - - ln -s '$b' reads.bam && - ln -s '${b.metadata.bam_index}' reads.bam.bai && - #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' genome.fa && - #else: - ln -f -s '$reference_source.ref_file.fields.path' genome.fa && - #end if + @PREPROCESS_INPUTS@ nanopolish variants -r reads.fasta @@ -89,11 +57,11 @@ --models-fofn '$input_models_fofn' #end if - && - - nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa - - + && + nanopolish vcf2fasta + --skip-checks + -g genome.fa + variants.vcf > polished.fa ]]></command> <inputs> <!-- index inputs --> @@ -131,7 +99,6 @@ </section> <!-- optional params --> - <!-- optional params --> <param argument="-w" type="text" optional="true" label="find variants in window of region chromsome:start-end" /> <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/> @@ -251,8 +218,7 @@ <help><![CDATA[ Build an index mapping from basecalled reads to the signals measured by the sequencer - and - Find SNPs using a signal-level HMM + and find SNPs using a signal-level HMM. Tutorial and manual available at: http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html |