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comparison bealign.xml @ 1:f9b72a376ec9 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit 9a163dd8880c14f371e2603389f4951881a74b25"
author iuc
date Thu, 13 May 2021 16:57:26 +0000
parents 6ef10b28e967
children d8b6f0adaa79
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0:6ef10b28e967 1:f9b72a376ec9
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command>bealign --version</version_command> 8 <version_command>bealign --version</version_command>
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might
12 ## break if there are non-standard characters in the sequences or text other
13 ## than alphanumerics in the sequence names, so we run the input dataset
14 ## through a simple awk script to remove any non-IUPAC-standard nucleotides
15 ## and replace any unwanted characters in the sequence names with underscores.
16 ## This should not affect the actual alignment, since any non-standard character
17 ## in the sequences is already ignored, but the possibility remains.
18 cat '$input' | awk '{ if (\$0 ~ "^[^>]") {a = gensub(/[^ACGTURYKMSWBDHVNacgturykmswbdhvn?-]/, "", "g"); } else {a=gensub(/[^>A-Za-z0-9_]/, "_", "g"); }; print a } ' |
19 sed 's,_\\+,_,g' > reads.fa &&
11 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet 20 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
12 #if $advanced.expected_identity: 21 #if $advanced.expected_identity:
13 --expected-identity $advanced.expected_identity 22 --expected-identity $advanced.expected_identity
14 #end if 23 #end if
15 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference 24 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
16 #if $advanced.discard: 25 #if $advanced.discard:
17 $advanced.discard '$advanced.discarded_reads' 26 $advanced.discard '$advanced.discarded_reads'
18 #end if 27 #end if
19 '$input' '$output' 28 reads.fa alignment.bam
20 ]]> 29 ]]>
21 </command> 30 </command>
22 <inputs> 31 <inputs>
23 <param name="input" type="data" format="fasta" label="Input reads" /> 32 <param name="input" type="data" format="fasta" label="Input reads" help="For the benefit of certain tools that depend on this aligner, such as the TN-93 clustering tool, this dataset's sequence names will have non-alphanumeric characters replaced with underscores, and the sequences will be restricted to the set of IUPAC nucleotide characters." />
24 <conditional name="select_reference"> 33 <conditional name="select_reference">
25 <param name="reference_type" type="select"> 34 <param name="reference_type" type="select">
26 <option value="preset">Select preset</option> 35 <option value="preset">Select preset</option>
27 <option value="dataset">Use a history dataset</option> 36 <option value="dataset">Use a history dataset</option>
28 </param> 37 </param>
70 <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" /> 79 <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
71 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" /> 80 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
72 </section> 81 </section>
73 </inputs> 82 </inputs>
74 <outputs> 83 <outputs>
75 <data name="output" format="bam" /> 84 <data name="output" format="bam" from_work_dir="alignment.bam" />
76 <data name="discarded_reads" format="fasta"> 85 <data name="discarded_reads" format="fasta">
77 <filter>advanced['discard']</filter> 86 <filter>advanced['discard']</filter>
78 </data> 87 </data>
79 </outputs> 88 </outputs>
80 <tests> 89 <tests>
81 <test> 90 <test>
82 <param name="input" ftype="fasta" value="bealign-in1.fa" /> 91 <param name="input" ftype="fasta" value="bealign-in1.fa" />
83 <param name="reference_type" value="dataset" /> 92 <param name="reference_type" value="dataset" />
84 <param name="score_matrix" value="HIV_BETWEEN_F" /> 93 <param name="score_matrix" value="HIV_BETWEEN_F" />
85 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" /> 94 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
86 <output name="output" file="bealign-out1.bam" /> 95 <output name="output" file="bealign-out1.bam" ftype="bam" />
87 </test> 96 </test>
88 <test> 97 <test>
89 <param name="input" ftype="fasta" value="bealign-in2.fa" /> 98 <param name="input" ftype="fasta" value="bealign-in2.fa" />
90 <param name="reference_type" value="dataset" /> 99 <param name="reference_type" value="dataset" />
91 <param name="score_matrix" value="BLOSUM62" /> 100 <param name="score_matrix" value="BLOSUM62" />
92 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> 101 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
93 <output name="output" file="bealign-out2.bam" /> 102 <output name="output" file="bealign-out2.bam" ftype="bam" />
94 </test> 103 </test>
95 <test> 104 <test>
96 <param name="input" ftype="fasta" value="bealign-in2.fa" /> 105 <param name="input" ftype="fasta" value="bealign-in2.fa" />
97 <param name="reference_type" value="dataset" /> 106 <param name="reference_type" value="dataset" />
98 <param name="expected_identity" value="0.9" /> 107 <param name="expected_identity" value="0.9" />
99 <param name="score_matrix" value="BLOSUM62" /> 108 <param name="score_matrix" value="BLOSUM62" />
100 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> 109 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
101 <output name="output" file="bealign-out3.bam" /> 110 <output name="output" file="bealign-out3.bam" ftype="bam" />
102 </test> 111 </test>
103 </tests> 112 </tests>
104 <help> 113 <help>
105 <![CDATA[ 114 <![CDATA[
106 bealign 115 bealign