Mercurial > repos > thanhlv > polypolish
comparison polypolish.xml @ 1:a38f6a0ebbf9 draft
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit f361210f97bf2dfa63c2267193eca3163e17f78a-dirty"
author | thanhlv |
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date | Fri, 23 Sep 2022 23:26:59 +0000 |
parents | 3c7cbfb8f43d |
children | 96580cd76488 |
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0:3c7cbfb8f43d | 1:a38f6a0ebbf9 |
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3 <macros> | 3 <macros> |
4 <token name="@VERSION@">0.5.0</token> | 4 <token name="@VERSION@">0.5.0</token> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="@VERSION@">polypolish</requirement> | 7 <requirement type="package" version="@VERSION@">polypolish</requirement> |
8 <requirement type="package" version="1.15.1">samtools</requirement> | 8 <!--<requirement type="package" version="1.15.1">samtools</requirement> --> |
9 <requirement type="package" version="0.7.17">bwa</requirement> | 9 <requirement type="package" version="0.7.17">bwa</requirement> |
10 </requirements> | 10 </requirements> |
11 <version_command>polypolish --version</version_command> | 11 <version_command>polypolish --version</version_command> |
12 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
13 #if $short_reads.sr_type == 'paired' | 13 #if $short_reads.sr_type == 'paired' |
14 ln -s '$short_read.R1' reads_1.fastq.gz && | 14 ln -s '$short_reads.R1' reads_1.fastq.gz && |
15 ln -s '$short_read.R2' reads_2.fastq.gz && | 15 ln -s '$short_reads.R2' reads_2.fastq.gz && |
16 #else if str($short_reads.sr_type) == "collection" | 16 #else if str($short_reads.sr_type) == "collection" |
17 ln -s '$short_read.input1.forward' reads_1.fastq.gz && | 17 ln -s '$short_reads.input1.forward' reads_1.fastq.gz && |
18 ln -s '$short_read.input1.reverse' reads_2.fastq.gz && | 18 ln -s '$short_reads.input1.reverse' reads_2.fastq.gz && |
19 #end if | 19 #end if |
20 | 20 |
21 ln -s '${assembly}' draft.fa && | 21 ln -s '${assembly}' draft.fa && |
22 bwa index draft.fa && | 22 bwa index draft.fa && |
23 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_1.fastq.gz > alignments_1.sam && | 23 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_1.fastq.gz > alignments_1.sam && |
24 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_2.fastq.gz > alignments_2.sam && | 24 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_2.fastq.gz > alignments_2.sam && |
25 polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam && | 25 polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam && |
26 polypolish | 26 polypolish |
27 #if $debug | 27 #if $debug |
28 $debug debug.tsv | 28 $debug debug.tsv |
29 #end if | 29 #end if |
30 -d ${min_depth} | 30 -d ${min_depth} |
31 -i ${fraction_invalid} | 31 -i ${fraction_invalid} |
32 -m ${max_errors} | 32 -m ${max_errors} |
33 -v ${fraction_valid} | 33 -v ${fraction_valid} |
34 draft.fasta filtered_1.sam filtered_2.sam | 34 draft.fasta filtered_1.sam filtered_2.sam |
35 > polished.fasta | 35 > polished.fasta |
36 ]]> </command> | 36 ]]> </command> |
37 | 37 |
38 <inputs> | 38 <inputs> |
39 <param name="basecalled" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Basecalled data"/> | 39 <param name="assembly" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Assembly"/> |
40 <conditional name="short_reads"> | 40 <conditional name="short_reads"> |
41 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> | 41 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> |
42 <option value="paired" selected="true">Paired End</option> | 42 <option value="paired" selected="true">Paired End</option> |
43 <option value="collection">Paired Collection</option> | 43 <option value="collection">Paired Collection</option> |
44 </param> | 44 </param> |
50 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> | 50 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> |
51 </when> | 51 </when> |
52 </conditional> | 52 </conditional> |
53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" /> | 53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" /> |
54 <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" /> | 54 <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" /> |
55 <param argument="fraction_valid" type="integer" value="10" min="1" label="Ignore alignments with more than this many mismatches and indels" /> | 55 <param argument="fraction_valid" type="integer" value="0.2" min="0.0" max="1.0" label="Ignore alignments with more than this many mismatches and indels" /> |
56 <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" /> | 56 <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" /> |
57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" /> | 57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" /> |
58 </inputs> | 58 </inputs> |
59 <outputs> | 59 <outputs> |
60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" /> | 60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" /> |