Mercurial > repos > bgruening > nanopolish_eventalign
changeset 8:3b6f94fc7e1d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
| author | bgruening |
|---|---|
| date | Thu, 30 Nov 2023 17:58:54 +0000 |
| parents | 85a394edc247 |
| children | |
| files | macros.xml nanopolish_eventalign.xml |
| diffstat | 2 files changed, 97 insertions(+), 64 deletions(-) [+] |
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--- a/macros.xml Fri Jul 30 06:28:28 2021 +0000 +++ b/macros.xml Thu Nov 30 17:58:54 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 '$reference_source.ref_file.fields.path' genome.fa && + #end if + ]]></token> + <xml name="citations"> <citations> <citation type="doi">10.1038/nmeth.3444</citation>
--- a/nanopolish_eventalign.xml Fri Jul 30 06:28:28 2021 +0000 +++ b/nanopolish_eventalign.xml Thu Nov 30 17:58:54 2023 +0000 @@ -1,74 +1,42 @@ -<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy1"> +<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Align nanopore events to reference k-mers</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$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 '$reference_source.ref_file.fields.path' genome.fa && - #end if + @PREPROCESS_INPUTS@ nanopolish eventalign - -r reads.fasta - -b reads.bam - -g genome.fa - #if str($min_mapping_quality): - -q $min_mapping_quality - #end if - --threads "\${GALAXY_SLOTS:-4}" - $samples - $scale_events - $signal_index - $sam - $print_read_names - #if $w and str($w).strip(): - -w "${w}" - #end if - #if $input_models_fofn: - --models-fofn '$input_models_fofn' - #end if - #if $summary: - --summary eventalign-summary.txt - #end if - > eventalign.out + -r reads.fasta + -b reads.bam + -g genome.fa + #if str($min_mapping_quality): + -q $min_mapping_quality + #end if + --threads "\${GALAXY_SLOTS:-4}" + $samples + $scale_events + $signal_index + $sam + $print_read_names + #if $w and str($w).strip(): + -w "${w}" + #end if + #if $input_models_fofn: + --models-fofn '$input_models_fofn' + #end if + #if $summary: + --summary eventalign-summary.txt + #end if + > eventalign.out ]]></command> <inputs> <!-- index inputs --> <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> - <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> + <param type="data" name="input_reads_raw" format="fast5.tar.xz,fast5.tar.gz,fast5.tar.bz2,fast5.tar,fast5" label="Flat archive file of raw fast5 files"/> <!-- variants consensus inputs --> <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> @@ -109,17 +77,16 @@ label="Summarize the alignment of each read/strand" /> <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" label="Write the raw samples for the event to the tsv output" /> - <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" + <param argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" label="Scale events to the model, rather than vice-versa" /> - <param name="signal_index" argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" + <param argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" label="write the raw signal start and end index values for the event to the tsv output" /> <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" label="write output in SAM format" /> - <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" + <param argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" label="Print read names instead of indexes" /> - </inputs> <outputs> @@ -136,8 +103,25 @@ <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-200010" /> <param name="sam" value="true" /> - <output name="output_summary" file="eventalign-summary.txt" /> - <output name="output_eventalign" file="reads-draft.eventalign.sam"/> + <output name="output_summary" file="eventalign-summary.txt" compare="sim_size"> + <assert_contents> + <has_n_lines n="144"/> + <has_n_columns n="14"/> + <has_line_matching expression="read_index\sread_name\sfast5_path\smodel_name\sstrand\snum_events\snum_steps\snum_skips\snum_stays\stotal_duration\sshift\sscale\sdrift\svar"/> + <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> + <has_text text="15727"/> + <has_text text="fast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read5665_strand.fast5"/> + </assert_contents> + </output> + <output name="output_eventalign" file="reads-draft.eventalign.sam" compare="sim_size"> + <assert_contents> + <has_n_lines n="148"/> + <has_line_matching expression="@SQ\sSN:tig00000001\sLN:4376233"/> + <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> + <has_text text="191118"/> + <has_text text="274S1M2I3M1I2M2I9M1I1M1I1M1I9M6I3M1I1M2I2M2I2M1"/> + </assert_contents> + </output> </test> <test> <param name="input_merged" ftype="fasta" value="reads.fasta" />