Mercurial > repos > iuc > bioext_bealign
comparison bealign.xml @ 8:8a7462c0ac14 draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988
author | iuc |
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date | Sun, 25 Feb 2024 19:30:06 +0000 |
parents | a07a2d9ddd42 |
children | 396cc0c65700 |
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7:a07a2d9ddd42 | 8:8a7462c0ac14 |
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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="1.19.2">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"/> |