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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
author iuc
date Thu, 24 Oct 2024 18:10:50 +0000
parents 36c91ff33d70
children
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4:36c91ff33d70 5:d6d746d0d1d0
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">varvamp</xref> 7 <xref type="bio.tools">varvamp</xref>
8 </xrefs> 8 </xrefs>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
11 <requirement type="package" version="2.0.1">primer3-py</requirement> 11 <requirement type="package" version="2.0.3">primer3-py</requirement>
12 <requirement type="package" version="0.7.17">seqfold</requirement> 12 <requirement type="package" version="0.7.17">seqfold</requirement>
13 <requirement type="package" version="3.12">python</requirement>
14 <requirement type="package" version="9.5">coreutils</requirement>
13 </requirements> 15 </requirements>
14 <version_command>varvamp --version</version_command> 16 <version_command>varvamp --version</version_command>
15 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
16 VARVAMP_CONFIG=custom_config varvamp 18 VARVAMP_CONFIG=custom_config varvamp
17 19
18 $mode.m_select 20 $mode.m_select
21 --name '$mode.name'
19 #if $mode.main_params.specify_how in ("set_threshold", "set_both"): 22 #if $mode.main_params.specify_how in ("set_threshold", "set_both"):
20 --threshold $mode.main_params.threshold 23 --threshold $mode.main_params.threshold
21 #end if 24 #end if
22 #if $mode.main_params.specify_how in ("set_n_ambig", "set_both"): 25 #if $mode.main_params.specify_how in ("set_n_ambig", "set_both"):
23 --n-ambig $mode.main_params.n_ambig 26 --n-ambig $mode.main_params.n_ambig
45 --threads \${GALAXY_SLOTS:-1} 48 --threads \${GALAXY_SLOTS:-1}
46 49
47 '$alignment' 50 '$alignment'
48 results/ 51 results/
49 52
53 #if $mode.scheme_outputs and 'primer_binding_sites' in $mode.scheme_outputs:
54 ## the leading header line written by this version of the tool
55 ## is less than helpful in that in can cause parsing issues with downstream tools like ivar trim
56 && tail -n +2 results/primers.bed > results/primers_headerless.bed
57 #end if
50 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs: 58 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:
51 ## make the primer sequences fasta discoverable under the same name that is used in "single" mode 59 ## make the primer sequences fasta discoverable under the same name that is used in "single" mode
52 && mv results/oligos.fasta results/primers.fasta 60 && mv results/oligos.fasta results/primers.fasta
53 #end if 61 #end if
54 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs: 62 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
55 ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output 63 ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output
56 && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv 64 && cp --update=none dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
57 #end if 65 #end if
58 ]]></command> 66 ]]></command>
59 <configfiles> 67 <configfiles>
60 <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes": 68 <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes":
61 PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt) 69 PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt)
116 <option value="single">Primers for single amplicons (single)</option> 124 <option value="single">Primers for single amplicons (single)</option>
117 <option value="tiled">Tiled primer scheme for whole-genome sequencing (tiled)</option> 125 <option value="tiled">Tiled primer scheme for whole-genome sequencing (tiled)</option>
118 <option value="qpcr">qPCR primers (qpcr)</option> 126 <option value="qpcr">qPCR primers (qpcr)</option>
119 </param> 127 </param>
120 <when value="single"> 128 <when value="single">
129 <param argument="--name" type="text" value="AMPLICON" label="Name your amplicon" help="This name will be used in various outputs of the tool." />
121 <expand macro="main_parameters" /> 130 <expand macro="main_parameters" />
122 <expand macro="amplicon_length_restrictions" /> 131 <expand macro="amplicon_length_restrictions" />
123 <expand macro="blast_options" /> 132 <expand macro="blast_options" />
124 <conditional name="limit_report"> 133 <conditional name="limit_report">
125 <param name="choice" type="select" label="Limit the number of amplicons to report?"> 134 <param name="choice" type="select" label="Limit the number of amplicons to report?">
140 <expand macro="miscellaneous_outputs"> 149 <expand macro="miscellaneous_outputs">
141 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option> 150 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>
142 </expand> 151 </expand>
143 </when> 152 </when>
144 <when value="tiled"> 153 <when value="tiled">
154 <param argument="--name" type="text" value="TILED_SCHEME" label="Name your primer scheme" help="This name will be used in various outputs of the tool." />
145 <expand macro="main_parameters" /> 155 <expand macro="main_parameters" />
146 <expand macro="amplicon_length_restrictions" /> 156 <expand macro="amplicon_length_restrictions" />
147 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" /> 157 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" />
148 <expand macro="blast_options" /> 158 <expand macro="blast_options" />
149 <expand macro="customize_advanced" /> 159 <expand macro="customize_advanced" />
156 <expand macro="miscellaneous_outputs"> 166 <expand macro="miscellaneous_outputs">
157 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option> 167 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>
158 </expand> 168 </expand>
159 </when> 169 </when>
160 <when value="qpcr"> 170 <when value="qpcr">
171 <param argument="--name" type="text" value="QPCR_SCHEME" label="Name your qPCR scheme" help="This name will be used in various outputs of the tool." />
161 <expand macro="main_parameters"> 172 <expand macro="main_parameters">
162 <param argument="--pn-ambig" type="integer" min="0" value="1" label="Maximum number of ambiguous nucleotides per qPCR probe to be tolerated" help="To enforce specificity of detection, varVAMP will refuse to work if you set this value higher than for the amplicon primers above, and you may actually want to set it slightly lower than that value." /> 173 <param argument="--pn-ambig" type="integer" min="0" value="1" label="Maximum number of ambiguous nucleotides per qPCR probe to be tolerated" help="To enforce specificity of detection, varVAMP will refuse to work if you set this value higher than for the amplicon primers above, and you may actually want to set it slightly lower than that value." />
163 </expand> 174 </expand>
164 <param argument="--test-n" type="integer" min="1" value="50" label="Top n qPCR amplicons to test" help="test the top n qPCR amplicons for secondary structures at the minimal primer temperature. (default: 50)" /> 175 <param argument="--test-n" type="integer" min="1" value="50" label="Top n qPCR amplicons to test" help="test the top n qPCR amplicons for secondary structures at the minimal primer temperature. (default: 50)" />
165 <param argument="--deltaG" type="integer" value="-3" label="Minimum free energy (kcal/mol/K) cutoff" help="Minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temperature. (default: -3." /> 176 <param argument="--deltaG" type="integer" value="-3" label="Minimum free energy (kcal/mol/K) cutoff" help="Minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temperature. (default: -3." />
208 <data name="primer_seqs" format="fasta" from_work_dir="results/primers.fasta" label="${tool.name} on ${on_string}: Sequences of designed oligos"> 219 <data name="primer_seqs" format="fasta" from_work_dir="results/primers.fasta" label="${tool.name} on ${on_string}: Sequences of designed oligos">
209 <filter>mode['m_select'] in ('single', 'qpcr') and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter> 220 <filter>mode['m_select'] in ('single', 'qpcr') and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
210 </data> 221 </data>
211 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences"> 222 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">
212 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter> 223 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
213 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_0.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" /> 224 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
214 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" /> 225 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_2.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
215 </collection> 226 </collection>
216 <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites"> 227 <data name="primers_bed" format="bed" from_work_dir="results/primers_headerless.bed" label="${tool.name} on ${on_string}: Primer binding sites">
217 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter> 228 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
218 </data> 229 </data>
219 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations"> 230 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
220 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter> 231 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter>
221 </data> 232 </data>
342 </output> 353 </output>
343 <output_collection name="primer_seqs_collection" type="list" count="2"> 354 <output_collection name="primer_seqs_collection" type="list" count="2">
344 <element name="pool1_sequences" ftype="fasta"> 355 <element name="pool1_sequences" ftype="fasta">
345 <assert_contents> 356 <assert_contents>
346 <has_n_lines n="4"/> 357 <has_n_lines n="4"/>
347 <has_line line=">AMPLICON_0_LEFT"/> 358 <has_line line=">TILED_SCHEME_0_LEFT"/>
348 </assert_contents> 359 </assert_contents>
349 </element> 360 </element>
350 <element name="pool2_sequences" ftype="fasta"> 361 <element name="pool2_sequences" ftype="fasta">
351 <assert_contents> 362 <assert_contents>
352 <has_n_lines n="4"/> 363 <has_n_lines n="4"/>
353 <has_line line=">AMPLICON_1_LEFT"/> 364 <has_line line=">TILED_SCHEME_1_LEFT"/>
354 </assert_contents> 365 </assert_contents>
355 </element> 366 </element>
356 </output_collection> 367 </output_collection>
357 </test> 368 </test>
358 <test expect_num_outputs="9"> 369 <test expect_num_outputs="9">