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comparison varvamp.xml @ 6:c1f08498cd74 draft default tip

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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805
author iuc
date Thu, 13 Feb 2025 09:20:17 +0000
parents d6d746d0d1d0
children
comparison
equal deleted inserted replaced
5:d6d746d0d1d0 6:c1f08498cd74
48 --threads \${GALAXY_SLOTS:-1} 48 --threads \${GALAXY_SLOTS:-1}
49 49
50 '$alignment' 50 '$alignment'
51 results/ 51 results/
52 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
58 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs: 53 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:
59 ## make the primer sequences fasta discoverable under the same name that is used in "single" mode 54 ## make the primer sequences fasta discoverable under the same name that is used in "single" mode
60 && mv results/oligos.fasta results/primers.fasta 55 && mv results/oligos.fasta results/primers.fasta
61 #end if 56 #end if
62 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs: 57 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
152 </when> 147 </when>
153 <when value="tiled"> 148 <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." /> 149 <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." />
155 <expand macro="main_parameters" /> 150 <expand macro="main_parameters" />
156 <expand macro="amplicon_length_restrictions" /> 151 <expand macro="amplicon_length_restrictions" />
157 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" /> 152 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicon inserts" help="default: 100" />
158 <expand macro="blast_options" /> 153 <expand macro="blast_options" />
159 <expand macro="customize_advanced" /> 154 <expand macro="customize_advanced" />
160 <expand macro="primer_scheme_outputs"> 155 <expand macro="primer_scheme_outputs">
161 <option value="amplicon_assignment" selected="true">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line; required input for automated primer trimming in some downstream analysis workflows</option> 156 <option value="amplicon_assignment" selected="true">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line; required input for automated primer trimming in some downstream analysis workflows</option>
162 <option value="primer_dimers" selected="true">If any primers in the tiling scheme are predicted to form primer dimers, details about these will be found in this tabular output.</option> 157 <option value="primer_dimers" selected="true">If any primers in the tiling scheme are predicted to form primer dimers, details about these will be found in this tabular output.</option>
222 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences"> 217 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">
223 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter> 218 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
224 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" /> 219 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
225 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_2.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" /> 220 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_2.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
226 </collection> 221 </collection>
227 <data name="primers_bed" format="bed" from_work_dir="results/primers_headerless.bed" label="${tool.name} on ${on_string}: Primer binding sites"> 222 <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">
228 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter> 223 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
229 </data> 224 </data>
230 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations"> 225 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
231 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter> 226 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter>
232 </data> 227 </data>
325 <param name="threshold" value="0.6"/> 320 <param name="threshold" value="0.6"/>
326 <param name="n_ambig" value="2"/> 321 <param name="n_ambig" value="2"/>
327 </conditional> 322 </conditional>
328 <param name="opt_length" value="150"/> 323 <param name="opt_length" value="150"/>
329 <param name="max_length" value="300"/> 324 <param name="max_length" value="300"/>
330 <param name="overlap" value="100"/> 325 <param name="overlap" value="76"/>
331 </conditional> 326 </conditional>
332 <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" /> 327 <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />
333 <output name="primers_bed" ftype="bed"> 328 <output name="primers_bed" ftype="bed">
334 <assert_contents> 329 <assert_contents>
335 <has_n_lines n="4" /> 330 <has_n_lines n="4" />