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comparison nanopolish_polya.xml @ 5:4857d5bcce52 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:59:18 +0000
parents be717b65851f
children
comparison
equal deleted inserted replaced
4:d376944466bf 5:4857d5bcce52
1 <tool id="nanopolish_polya" name="Nanopolish polyA" version="@VERSION@+galaxy0"> 1 <tool id="nanopolish_polya" name="Nanopolish polyA" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Estimate the length of the poly-A tail on direct RNA reads.</description> 2 <description>- Estimate the length of the poly-A tail on direct RNA reads.</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 polya 10 nanopolish polya
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 --threads "\${GALAXY_SLOTS:-4}" 14 --threads "\${GALAXY_SLOTS:-4}"
47 #if $w and str($w).strip(): 15 #if $w and str($w).strip():
48 -w "${w}" 16 -w "${w}"
49 #end if 17 #end if
50 > polya_results.tsv 18 > polya_results.tsv
51 ]]></command> 19 ]]></command>
52 <inputs> 20 <inputs>
53 <!-- index inputs --> 21 <!-- index inputs -->
54 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 22 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
91 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" /> 59 <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" /> 60 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
93 <param name="reference_source_selector" value="history" /> 61 <param name="reference_source_selector" value="history" />
94 <param name="ref_file" value="enolase_reference.fas" /> 62 <param name="ref_file" value="enolase_reference.fas" />
95 <!-- <param name="w" value="tig00000001:200000-202000" /> --> 63 <!-- <param name="w" value="tig00000001:200000-202000" /> -->
96 <output name="polya_results" file="30xpolyA-small-subset-results.tsv" /> 64 <output name="polya_results" file="30xpolyA-small-subset-results.tsv" compare="sim_size">
65 <assert_contents>
66 <has_n_lines n="14"/>
67 <has_n_columns n="10"/>
68 <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
69 <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
70 <has_text text="YHR174W"/>
71 <has_text text="READ_FAILED_LOAD"/>
72 </assert_contents>
73 </output>
97 </test> 74 </test>
98 <test> 75 <test>
99 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" /> 76 <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" /> 77 <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" /> 78 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
102 <param name="reference_source_selector" value="history" /> 79 <param name="reference_source_selector" value="history" />
103 <param name="ref_file" value="enolase_reference.fas" /> 80 <param name="ref_file" value="enolase_reference.fas" />
104 <param name="w" value="YHR174W:600-900" /> 81 <param name="w" value="YHR174W:600-900" />
105 <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" /> 82 <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" compare="sim_size">
83 <assert_contents>
84 <has_n_lines n="12"/>
85 <has_n_columns n="10"/>
86 <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
87 <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
88 <has_text text="YHR174W"/>
89 <has_text text="READ_FAILED_LOAD"/>
90 </assert_contents>
91 </output>
106 </test> 92 </test>
107 <test> 93 <test>
108 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" /> 94 <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" /> 95 <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" /> 96 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
111 <param name="reference_source_selector" value="history" /> 97 <param name="reference_source_selector" value="history" />
112 <param name="ref_file" value="enolase_reference.fas" /> 98 <param name="ref_file" value="enolase_reference.fas" />
113 <param name="w" value="YHR174W:600-900" /> 99 <param name="w" value="YHR174W:600-900" />
114 <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" /> 100 <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" compare="sim_size">
101 <assert_contents>
102 <has_n_lines n="12"/>
103 <has_n_columns n="10"/>
104 <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
105 <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
106 <has_text text="YHR174W"/>
107 <has_text text="READ_FAILED_LOAD"/>
108 </assert_contents>
109 </output>
115 </test> 110 </test>
116 </tests> 111 </tests>
117 <help><![CDATA[ 112 <help><![CDATA[
118 Usage: nanopolish polya [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa 113 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 114 Estimate the length of the poly-A tail on direct RNA reads