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comparison nanopolish_polya.xml @ 0:7739a9b0dd83 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
author bgruening
date Wed, 19 Jun 2019 07:00:20 -0400
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children 449e9aeded2d
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-1:000000000000 0:7739a9b0dd83
1 <tool id="nanopolish_polya" name="Nanopolish polyA" version="0.1.0">
2 <description>- Estimate the length of the poly-A tail on direct RNA reads.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$input_merged' reads.fasta &&
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
42 nanopolish polya
43 -r reads.fasta
44 -b reads.bam
45 -g genome.fa
46 --threads "\${GALAXY_SLOTS:-4}"
47 #if $w and str($w).strip():
48 -w "${w}"
49 #end if
50 > polya_results.tsv
51 ]]></command>
52 <inputs>
53 <!-- index inputs -->
54 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
55 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
56
57 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
58 <conditional name="reference_source">
59 <param name="reference_source_selector" type="select" label="Load reference genome from">
60 <option value="cached">Local cache</option>
61 <option value="history">History</option>
62 </param>
63 <when value="cached">
64 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
65 <options from_data_table="all_fasta">
66 </options>
67 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
68 </param>
69 </when>
70 <when value="history">
71 <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" />
72 </when>
73 </conditional>
74
75 <section name="adv" title="Optional data inputs">
76 <!-- optional inputs -->
77 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
78 </section>
79
80 <param argument="-w" type="text" optional="true"
81 label="only compute the poly-A lengths for reads in window STR (format: ctg:start_id-end_id)" />
82
83 </inputs>
84
85 <outputs>
86 <data name="polya_results" format="tabular" from_work_dir="polya_results.tsv" label="called methylation sites" />
87 </outputs>
88 <tests>
89 <test>
90 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
91 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" />
92 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
93 <param name="reference_source_selector" value="history" />
94 <param name="ref_file" value="enolase_reference.fas" />
95 <!-- <param name="w" value="tig00000001:200000-202000" /> -->
96 <output name="polya_results" file="30xpolyA-small-subset-results.tsv" />
97 </test>
98 <test>
99 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
100 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" />
101 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
102 <param name="reference_source_selector" value="history" />
103 <param name="ref_file" value="enolase_reference.fas" />
104 <param name="w" value="YHR174W:600-900" />
105 <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" />
106 </test>
107 <test>
108 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
109 <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files_30xpolyA-small-subset.tar" />
110 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
111 <param name="reference_source_selector" value="history" />
112 <param name="ref_file" value="enolase_reference.fas" />
113 <param name="w" value="YHR174W:600-900" />
114 <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" />
115 </test>
116 </tests>
117 <help><![CDATA[
118 Usage: nanopolish polya [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
119 Estimate the length of the poly-A tail on direct RNA reads
120
121 Quickstart tutorial and manual available at:
122 http://nanopolish.readthedocs.io/en/latest/quickstart_polya.html
123
124 ]]></help>
125 <expand macro="citations" />
126 </tool>