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comparison bealign.xml @ 2:b22f3ccefaea draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
author iuc
date Fri, 09 Jul 2021 15:17:51 +0000
parents e44c8819b04f
children 4157eaf015f2
comparison
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1:e44c8819b04f 2:b22f3ccefaea
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0"> 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@">0</token>
6 </macros> 7 </macros>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 <version_command>bealign --version</version_command> 9 <version_command>bealign --version</version_command>
9 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
10 <![CDATA[ 11 <![CDATA[
49 <option value="HXB2_env">HXB2 envelope</option> 50 <option value="HXB2_env">HXB2 envelope</option>
50 <option value="HXB2_rt">HXB2 reverse transcriptase</option> 51 <option value="HXB2_rt">HXB2 reverse transcriptase</option>
51 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option> 52 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
52 <option value="HXB2_rev">HXB2 rev</option> 53 <option value="HXB2_rev">HXB2 rev</option>
53 <option value="HXB2_vpu">HXB2 vpu</option> 54 <option value="HXB2_vpu">HXB2 vpu</option>
55 <option value="CoV2-3C">SARS-CoV-2: 3C</option>
56 <option value="CoV2-S">SARS-CoV-2: Spike</option>
57 <option value="CoV2-E">SARS-CoV-2: Envelope</option>
58 <option value="CoV2-M">SARS-CoV-2: Membrane</option>
59 <option value="CoV2-N">SARS-CoV-2: Nucleoprotein</option>
60 <option value="CoV2-endornase">SARS-CoV-2: endornase</option>
61 <option value="CoV2-exonuclease">SARS-CoV-2: exonuclease</option>
62 <option value="CoV2-helicase">SARS-CoV-2: helicase</option>
63 <option value="CoV2-leader">SARS-CoV-2: leader</option>
64 <option value="CoV2-methyltransferase">SARS-CoV-2: methyltransferase</option>
65 <option value="CoV2-nsp2">SARS-CoV-2: nsp2</option>
66 <option value="CoV2-nsp3">SARS-CoV-2: nsp3</option>
67 <option value="CoV2-nsp4">SARS-CoV-2: nsp4</option>
68 <option value="CoV2-nsp6">SARS-CoV-2: nsp6</option>
69 <option value="CoV2-nsp7">SARS-CoV-2: nsp7</option>
70 <option value="CoV2-nsp8">SARS-CoV-2: nsp8</option>
71 <option value="CoV2-nsp9">SARS-CoV-2: nsp9</option>
72 <option value="CoV2-nsp10">SARS-CoV-2: nsp10</option>
73 <option value="CoV2-ORF1a">SARS-CoV-2: ORF1a</option>
74 <option value="CoV2-ORF1b">SARS-CoV-2: ORF1b</option>
75 <option value="CoV2-ORF3a">SARS-CoV-2: ORF3a</option>
76 <option value="CoV2-ORF5">SARS-CoV-2: ORF5</option>
77 <option value="CoV2-ORF6">SARS-CoV-2: ORF6</option>
78 <option value="CoV2-ORF7a">SARS-CoV-2: ORF7a</option>
79 <option value="CoV2-ORF7b">SARS-CoV-2: ORF7b</option>
80 <option value="CoV2-ORF8">SARS-CoV-2: ORF8</option>
81 <option value="CoV2-ORF10">SARS-CoV-2: ORF10</option>
82 <option value="CoV2-RdRp">SARS-CoV-2: RNA-dependent RNA polymerase</option>
54 </param> 83 </param>
55 </when> 84 </when>
56 <when value="dataset"> 85 <when value="dataset">
57 <param argument="--reference" type="data" format="fasta" label="Reference sequences" /> 86 <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
58 </when> 87 </when>
90 <test> 119 <test>
91 <param name="input" ftype="fasta" value="bealign-in1.fa" /> 120 <param name="input" ftype="fasta" value="bealign-in1.fa" />
92 <param name="reference_type" value="dataset" /> 121 <param name="reference_type" value="dataset" />
93 <param name="score_matrix" value="HIV_BETWEEN_F" /> 122 <param name="score_matrix" value="HIV_BETWEEN_F" />
94 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" /> 123 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
95 <output name="output" file="bealign-out1.bam" ftype="bam" /> 124 <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
96 </test> 125 </test>
97 <test> 126 <test>
98 <param name="input" ftype="fasta" value="bealign-in2.fa" /> 127 <param name="input" ftype="fasta" value="bealign-in2.fa" />
99 <param name="reference_type" value="dataset" /> 128 <param name="reference_type" value="dataset" />
100 <param name="score_matrix" value="BLOSUM62" /> 129 <param name="score_matrix" value="BLOSUM62" />
101 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> 130 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
102 <output name="output" file="bealign-out2.bam" ftype="bam" /> 131 <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>
103 </test> 132 </test>
104 <test> 133 <test>
105 <param name="input" ftype="fasta" value="bealign-in2.fa" /> 134 <param name="input" ftype="fasta" value="bealign-in2.fa" />
106 <param name="reference_type" value="dataset" /> 135 <param name="reference_type" value="dataset" />
107 <param name="expected_identity" value="0.9" /> 136 <param name="expected_identity" value="0.9" />
108 <param name="score_matrix" value="BLOSUM62" /> 137 <param name="score_matrix" value="BLOSUM62" />
109 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> 138 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
110 <output name="output" file="bealign-out3.bam" ftype="bam" /> 139 <output name="output" file="bealign-out3.bam" ftype="bam" lines_diff="2"/>
111 </test> 140 </test>
112 </tests> 141 </tests>
113 <help> 142 <help>
114 <![CDATA[ 143 <![CDATA[
115 bealign 144 bealign