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comparison bealign.xml @ 4:a287431cdf4f draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit c9002fa57e4d800f2c1c8d1dafbceb7681b0fcc2"
author iuc
date Tue, 05 Oct 2021 09:52:56 +0000
parents fb4975b507c6
children c239e93d9f04
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3:fb4975b507c6 4:a287431cdf4f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 2 <tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>to a reference using a codon alignment algorithm</description> 3 <description>to a reference using a codon alignment algorithm</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@VERSION_SUFFIX@">1</token> 6 <token name="@VERSION_SUFFIX@">2</token>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="5.1.0">gawk</requirement> 9 <requirement type="package" version="5.1.0">gawk</requirement>
10 <requirement type="package" version="1.13">samtools</requirement>
10 </expand> 11 </expand>
11 <version_command>bealign --version</version_command> 12 <version_command>bealign --version</version_command>
12 <command detect_errors="exit_code"> 13 <command detect_errors="exit_code">
13 <![CDATA[ 14 <![CDATA[
14 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might 15 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might
16 ## than alphanumerics in the sequence names, so we run the input dataset 17 ## than alphanumerics in the sequence names, so we run the input dataset
17 ## through a simple awk script to remove any non-IUPAC-standard nucleotides 18 ## through a simple awk script to remove any non-IUPAC-standard nucleotides
18 ## and replace any unwanted characters in the sequence names with underscores. 19 ## and replace any unwanted characters in the sequence names with underscores.
19 ## This should not affect the actual alignment, since any non-standard character 20 ## This should not affect the actual alignment, since any non-standard character
20 ## in the sequences is already ignored, but the possibility remains. 21 ## in the sequences is already ignored, but the possibility remains.
22 set -o pipefail;
21 cat '$input' @SANITIZE@ reads.fa && 23 cat '$input' @SANITIZE@ reads.fa &&
22 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet 24 ## bealign's parallel job executor uses the NCPU env variable
25 NCPU=\${GALAXY_SLOTS:-2} bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
23 #if $advanced.expected_identity: 26 #if $advanced.expected_identity:
24 --expected-identity $advanced.expected_identity 27 --expected-identity $advanced.expected_identity
25 #end if 28 #end if
26 #if $advanced.discard: 29 #if $advanced.discard:
27 $advanced.discard '$advanced.discarded_reads' 30 $advanced.discard '$advanced.discarded_reads'
28 #end if 31 #end if
29 --score-matrix $advanced.score_matrix 32 --score-matrix $advanced.score_matrix
30 $advanced.reverse_complement 33 $advanced.reverse_complement
31 $advanced.keep_reference 34 $advanced.keep_reference
32 reads.fa '$output' 35 ## bypass bealign's internal pysam-based, single-threaded BAM sorting
33 #set $input_background = False 36 --no-sort
34 #if $background_source.selection == 'history': 37 reads.fa bealign_out.bam &&
35 #if $background_source.sequences: 38 samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' bealign_out.bam
36 #set $input_background = $background_source.sequences 39 #set $input_background = False
37 #end if 40 #if $background_source.selection == 'history':
38 #else: 41 #if $background_source.sequences:
39 #if $background_source.sequences: 42 #set $input_background = $background_source.sequences
40 #set $input_background = $background_source.sequences.fields.path 43 #end if
41 #end if 44 #else:
42 #end if 45 #if $background_source.sequences:
43 #if $input_background: 46 #set $input_background = $background_source.sequences.fields.path
44 && cat '$input_background' @SANITIZE@ background.fa && 47 #end if
45 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet 48 #end if
46 #if $advanced.expected_identity: 49 #if $input_background:
47 --expected-identity $advanced.expected_identity 50 && cat '$input_background' @SANITIZE@ background.fa &&
48 #end if 51 NCPU=\${GALAXY_SLOTS:-2} bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
49 --keep-reference --score-matrix $advanced.score_matrix $advanced.reverse_complement 52 #if $advanced.expected_identity:
50 background.fa '$background' 53 --expected-identity $advanced.expected_identity
51 #end if 54 #end if
55 --keep-reference --score-matrix $advanced.score_matrix $advanced.reverse_complement
56 ## bypass bealign's internal pysam-based, single-threaded BAM sorting
57 --no-sort
58 background.fa bealign_background.bam &&
59 samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$background' bealign_background.bam
60 #end if
52 #set $reference_name = str($select_reference.reference) 61 #set $reference_name = str($select_reference.reference)
53 #if $select_reference.reference_type == 'preset' and $select_reference.save_reference: 62 #if $select_reference.reference_type == 'preset' and $select_reference.save_reference:
54 && python '$__tool_directory__/copy_reference.py' --reference '$reference_name' --dataset '$saved_reference' 63 && python '$__tool_directory__/copy_reference.py' --reference '$reference_name' --dataset '$saved_reference'
55 #end if 64 #end if
56 ]]> 65 ]]>