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comparison bealign.xml @ 8:2b4afdf6c04c draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
author iuc
date Mon, 02 Sep 2024 10:14:27 +0000
parents 3628c36b3207
children 480f01788210
comparison
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7:3628c36b3207 8:2b4afdf6c04c
1 <?xml version="1.0"?>
2 <tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <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> 2 <description>to a reference using a codon alignment algorithm</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 <token name="@VERSION_SUFFIX@">0</token>
7 </macros> 5 </macros>
8 <expand macro="requirements"> 6 <expand macro="requirements">
9 <requirement type="package" version="5.1.0">gawk</requirement> 7 <requirement type="package" version="5.3.0">gawk</requirement>
10 <requirement type="package" version="1.14">samtools</requirement> 8 <requirement type="package" version="1.20">samtools</requirement>
11 </expand> 9 </expand>
12 <version_command>bealign --version</version_command> 10 <version_command>bealign --version</version_command>
13 <command detect_errors="exit_code"> 11 <command detect_errors="exit_code">
14 <![CDATA[ 12 <![CDATA[
15 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might 13 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might
141 <param argument="--alphabet" type="select" label="Alphabet to use for alignment"> 139 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
142 <option value="codon" selected="True">Codon</option> 140 <option value="codon" selected="True">Codon</option>
143 <option value="dna">DNA</option> 141 <option value="dna">DNA</option>
144 <option value="amino">Amino acids</option> 142 <option value="amino">Amino acids</option>
145 </param> 143 </param>
146 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix"> 144 <param argument="--score-matrix" type="select" label="Parametrize using score matrix">
147 <option value="BLOSUM62" selected="True">Blocks substitution</option> 145 <option value="BLOSUM62" selected="True">Blocks substitution</option>
148 <option value="DNA65">DNA, 65% expected identity</option> 146 <option value="DNA65">DNA, 65% expected identity</option>
149 <option value="DNA70">DNA, 70% expected identity</option> 147 <option value="DNA70">DNA, 70% expected identity</option>
150 <option value="DNA88">DNA, 88% expected identity</option> 148 <option value="DNA88">DNA, 88% expected identity</option>
151 <option value="DNA80">DNA, 80% expected identity</option> 149 <option value="DNA80">DNA, 80% expected identity</option>
153 <option value="PAM200">PAM 200 substitution</option> 151 <option value="PAM200">PAM 200 substitution</option>
154 <option value="PAM250">PAM 250 substitution</option> 152 <option value="PAM250">PAM 250 substitution</option>
155 <option value="HIV_BETWEEN_F">HIV between+F</option> 153 <option value="HIV_BETWEEN_F">HIV between+F</option>
156 </param> 154 </param>
157 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" /> 155 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
158 <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" /> 156 <param argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
159 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" /> 157 <param argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
160 </section> 158 </section>
161 </inputs> 159 </inputs>
162 <outputs> 160 <outputs>
163 <data name="output" format="bam" label="${tool.name} on ${on_string} - Aligned Sequences" /> 161 <data name="output" format="bam" label="${tool.name} on ${on_string} - Aligned Sequences" />
164 <data name="background" format="bam" label="${tool.name} on ${on_string} - Background" > 162 <data name="background" format="bam" label="${tool.name} on ${on_string} - Background" >
165 <filter>background_source['sequences']</filter> 163 <filter>background_source['sequences']</filter>
166 </data> 164 </data>
167 <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" > 165 <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" >
168 <filter>select_reference['save_reference']</filter> 166 <filter>select_reference['reference_type'] == 'preset' and select_reference['save_reference']</filter>
169 </data> 167 </data>
170 <data name="discarded_reads" format="fasta"> 168 <data name="discarded_reads" format="fasta">
171 <filter>advanced['discard']</filter> 169 <filter>advanced['discard']</filter>
172 </data> 170 </data>
173 </outputs> 171 </outputs>
174 <tests> 172 <tests>
175 <test> 173 <test expect_num_outputs="1">
176 <param name="input" ftype="fasta" value="query.fa" /> 174 <param name="input" ftype="fasta" value="query.fa" />
177 <param name="reference_type" value="dataset" /> 175 <param name="reference_type" value="dataset" />
178 <param name="score_matrix" value="HIV_BETWEEN_F" /> 176 <param name="score_matrix" value="HIV_BETWEEN_F" />
179 <param name="reference" ftype="fasta" value="reference.fa" /> 177 <param name="reference" ftype="fasta" value="reference.fa" />
180 <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" /> 178 <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
181 </test> 179 </test>
182 <test> 180 <test expect_num_outputs="1">
183 <param name="input" ftype="fasta" value="query.fa" /> 181 <param name="input" ftype="fasta" value="query.fa" />
184 <param name="reference_type" value="preset" /> 182 <param name="reference_type" value="preset" />
185 <param name="reference" value="CoV2-nsp8" /> 183 <param name="reference" value="CoV2-nsp8" />
186 <param name="score_matrix" value="HIV_BETWEEN_F" /> 184 <param name="score_matrix" value="HIV_BETWEEN_F" />
187 <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/> 185 <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>