Mercurial > repos > bgruening > nanopolish_eventalign
comparison nanopolish_eventalign.xml @ 8:3b6f94fc7e1d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author | bgruening |
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date | Thu, 30 Nov 2023 17:58:54 +0000 |
parents | 855b7ba0ce9c |
children |
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7:85a394edc247 | 8:3b6f94fc7e1d |
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1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy1"> | 1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
2 <description>- Align nanopore events to reference k-mers</description> | 2 <description>- Align nanopore events to reference k-mers</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 ln -s '$input_merged' reads.fasta && | 8 @PREPROCESS_INPUTS@ |
9 | |
10 #if $input_reads_raw.extension == 'fast5': | |
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && | |
12 | |
13 #else if $input_reads_raw.extension == 'fast5.tar': | |
14 ln -s '$input_reads_raw' fast5_files.tar && | |
15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files && | |
16 | |
17 #else if $input_reads_raw.extension == 'fast5.tar.bz2': | |
18 ln -s '$input_reads_raw' fast5_files.tar.bz2 && | |
19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files && | |
20 | |
21 #else: | |
22 ln -s '$input_reads_raw' fast5_files.tar.gz && | |
23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && | |
24 | |
25 #end if | |
26 | |
27 nanopolish index | |
28 -d fast5_files/ | |
29 #if $adv.input_seq_summary: | |
30 -s '$adv.input_seq_summary' | |
31 #end if | |
32 reads.fasta && | |
33 | |
34 ln -s '$b' reads.bam && | |
35 ln -s '${b.metadata.bam_index}' reads.bam.bai && | |
36 #if $reference_source.reference_source_selector == 'history': | |
37 ln -f -s '$reference_source.ref_file' genome.fa && | |
38 #else: | |
39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa && | |
40 #end if | |
41 | 9 |
42 nanopolish eventalign | 10 nanopolish eventalign |
43 -r reads.fasta | 11 -r reads.fasta |
44 -b reads.bam | 12 -b reads.bam |
45 -g genome.fa | 13 -g genome.fa |
46 #if str($min_mapping_quality): | 14 #if str($min_mapping_quality): |
47 -q $min_mapping_quality | 15 -q $min_mapping_quality |
48 #end if | 16 #end if |
49 --threads "\${GALAXY_SLOTS:-4}" | 17 --threads "\${GALAXY_SLOTS:-4}" |
50 $samples | 18 $samples |
51 $scale_events | 19 $scale_events |
52 $signal_index | 20 $signal_index |
53 $sam | 21 $sam |
54 $print_read_names | 22 $print_read_names |
55 #if $w and str($w).strip(): | 23 #if $w and str($w).strip(): |
56 -w "${w}" | 24 -w "${w}" |
57 #end if | 25 #end if |
58 #if $input_models_fofn: | 26 #if $input_models_fofn: |
59 --models-fofn '$input_models_fofn' | 27 --models-fofn '$input_models_fofn' |
60 #end if | 28 #end if |
61 #if $summary: | 29 #if $summary: |
62 --summary eventalign-summary.txt | 30 --summary eventalign-summary.txt |
63 #end if | 31 #end if |
64 > eventalign.out | 32 > eventalign.out |
65 | 33 |
66 | 34 |
67 ]]></command> | 35 ]]></command> |
68 <inputs> | 36 <inputs> |
69 <!-- index inputs --> | 37 <!-- index inputs --> |
70 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> | 38 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> |
71 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> | 39 <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"/> |
72 | 40 |
73 <!-- variants consensus inputs --> | 41 <!-- variants consensus inputs --> |
74 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> | 42 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> |
75 <conditional name="reference_source"> | 43 <conditional name="reference_source"> |
76 <param name="reference_source_selector" type="select" label="Load reference genome from"> | 44 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
107 <!-- optional flags --> | 75 <!-- optional flags --> |
108 <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true" | 76 <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true" |
109 label="Summarize the alignment of each read/strand" /> | 77 label="Summarize the alignment of each read/strand" /> |
110 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" | 78 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" |
111 label="Write the raw samples for the event to the tsv output" /> | 79 label="Write the raw samples for the event to the tsv output" /> |
112 <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" | 80 <param argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" |
113 label="Scale events to the model, rather than vice-versa" /> | 81 label="Scale events to the model, rather than vice-versa" /> |
114 <param name="signal_index" argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" | 82 <param argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" |
115 label="write the raw signal start and end index values for the event to the tsv output" /> | 83 label="write the raw signal start and end index values for the event to the tsv output" /> |
116 | 84 |
117 | 85 |
118 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" | 86 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" |
119 label="write output in SAM format" /> | 87 label="write output in SAM format" /> |
120 <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" | 88 <param argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" |
121 label="Print read names instead of indexes" /> | 89 label="Print read names instead of indexes" /> |
122 | |
123 </inputs> | 90 </inputs> |
124 | 91 |
125 <outputs> | 92 <outputs> |
126 <!-- variants consensus outputs --> | 93 <!-- variants consensus outputs --> |
127 <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" /> | 94 <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" /> |
134 <param name="b" value="reads.sorted.bam" /> | 101 <param name="b" value="reads.sorted.bam" /> |
135 <param name="reference_source_selector" value="history" /> | 102 <param name="reference_source_selector" value="history" /> |
136 <param name="ref_file" value="draft.fa" /> | 103 <param name="ref_file" value="draft.fa" /> |
137 <param name="w" value="tig00000001:200000-200010" /> | 104 <param name="w" value="tig00000001:200000-200010" /> |
138 <param name="sam" value="true" /> | 105 <param name="sam" value="true" /> |
139 <output name="output_summary" file="eventalign-summary.txt" /> | 106 <output name="output_summary" file="eventalign-summary.txt" compare="sim_size"> |
140 <output name="output_eventalign" file="reads-draft.eventalign.sam"/> | 107 <assert_contents> |
108 <has_n_lines n="144"/> | |
109 <has_n_columns n="14"/> | |
110 <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"/> | |
111 <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> | |
112 <has_text text="15727"/> | |
113 <has_text text="fast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read5665_strand.fast5"/> | |
114 </assert_contents> | |
115 </output> | |
116 <output name="output_eventalign" file="reads-draft.eventalign.sam" compare="sim_size"> | |
117 <assert_contents> | |
118 <has_n_lines n="148"/> | |
119 <has_line_matching expression="@SQ\sSN:tig00000001\sLN:4376233"/> | |
120 <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> | |
121 <has_text text="191118"/> | |
122 <has_text text="274S1M2I3M1I2M2I9M1I1M1I1M1I9M6I3M1I1M2I2M2I2M1"/> | |
123 </assert_contents> | |
124 </output> | |
141 </test> | 125 </test> |
142 <test> | 126 <test> |
143 <param name="input_merged" ftype="fasta" value="reads.fasta" /> | 127 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
144 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> | 128 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
145 <param name="b" value="reads.sorted.bam" /> | 129 <param name="b" value="reads.sorted.bam" /> |