Mercurial > repos > iuc > irma

comparison irma.xml @ 1:736090e99c59 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402
author iuc
date Wed, 22 Jan 2025 14:10:33 +0000
parents 3d86c05cd838
children 69ce61289a2a
comparison
equal deleted inserted replaced
0:3d86c05cd838 1:736090e99c59
1 <tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> 1 <tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
2 <description>Construct robust assemblies of highly variable RNA viruses</description> 2 <description>Construct robust assemblies of highly variable RNA viruses</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.2.0</token> 4 <token name="@TOOL_VERSION@">1.2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">irma-virus</xref> 8 <xref type="bio.tools">irma-virus</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
124 <option value="FLU" selected="true">FLU</option> 124 <option value="FLU" selected="true">FLU</option>
125 <option value="FLU-utr">FLU-utr</option> 125 <option value="FLU-utr">FLU-utr</option>
126 <option value="FLU-pacbio">FLU-pacbio</option> 126 <option value="FLU-pacbio">FLU-pacbio</option>
127 </param> 127 </param>
128 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs"> 128 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs">
129 <option value="amended_consensus" selected="false">Amended consensus files: Include ambiguity codes for alleles, with second allele frequency greater 0.25</option>
129 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option> 130 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option>
130 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option> 131 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option>
132 <option value="run_info" selected="false">Run info: Text file with run metadata</option>
131 </param> 133 </param>
132 <conditional name="advanced_config"> 134 <conditional name="advanced_config">
133 <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in IRMA's default configuration file."> 135 <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in IRMA's default configuration file.">
134 <option value="no">No, use defaults for advanced settings</option> 136 <option value="no">No, use defaults for advanced settings</option>
135 <option value="yes">Yes</option> 137 <option value="yes">Yes</option>
265 </when> 267 </when>
266 </conditional> 268 </conditional>
267 </inputs> 269 </inputs>
268 <outputs> 270 <outputs>
269 <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences"> 271 <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences">
272 <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/>
270 <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/> 273 <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/>
271 <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/>
272 <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/> 274 <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/>
273 <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/> 275 <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/>
274 <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/> 276 <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/>
275 <data name="NA" format="fasta" from_work_dir="resultDir/A_NA.fasta" label="NA"/> 277 <data name="NA" format="fasta" from_work_dir="resultDir/A_NA.fasta" label="NA"/>
276 <data name="MP" format="fasta" from_work_dir="resultDir/A_MP.fasta" label="MP"/> 278 <data name="MP" format="fasta" from_work_dir="resultDir/A_MP.fasta" label="MP"/>
277 <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/> 279 <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/>
278 </collection> 280 </collection>
279 <!-- optional outputs--> 281 <!-- optional outputs-->
282 <collection name="amended_collection" type="list" label="Amended Fasta Consensus">
283 <filter>optional_outputs and 'amended_consensus' in optional_outputs</filter>
284 <data name="PB2" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_1.fa" label="PB2"/>
285 <data name="PB1" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_2.fa" label="PB1"/>
286 <data name="PA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_3.fa" label="PA"/>
287 <data name="HA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_4.fa" label="HA"/>
288 <data name="NP" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_5.fa" label="NP"/>
289 <data name="NA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_6.fa" label="NA"/>
290 <data name="MP" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_7.fa" label="MP"/>
291 <data name="NS" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_8.fa" label="NS"/>
292 </collection>
280 <collection name="bam_collection" type="list" label="Alignment files (bam)"> 293 <collection name="bam_collection" type="list" label="Alignment files (bam)">
281 <filter>optional_outputs and 'bam' in optional_outputs</filter> 294 <filter>optional_outputs and 'bam' in optional_outputs</filter>
295 <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
282 <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/> 296 <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/>
283 <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
284 <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/> 297 <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/>
285 <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/> 298 <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/>
286 <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/> 299 <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/>
287 <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/> 300 <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/>
288 <data name="MP" format="bam" from_work_dir="resultDir/A_MP.bam" label="MP"/> 301 <data name="MP" format="bam" from_work_dir="resultDir/A_MP.bam" label="MP"/>
289 <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/> 302 <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/>
290 </collection> 303 </collection>
291 <collection name="vcf_collection" type="list" label="Variant calling files (VCF)"> 304 <collection name="vcf_collection" type="list" label="Variant calling files (VCF)">
292 <filter>optional_outputs and 'vcf' in optional_outputs</filter> 305 <filter>optional_outputs and 'vcf' in optional_outputs</filter>
306 <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
293 <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/> 307 <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
294 <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
295 <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/> 308 <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/>
296 <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/> 309 <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/>
297 <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/> 310 <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/>
298 <data name="NA" format="vcf" from_work_dir="resultDir/A_NA.vcf" label="NA"/> 311 <data name="NA" format="vcf" from_work_dir="resultDir/A_NA.vcf" label="NA"/>
299 <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/> 312 <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/>
300 <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/> 313 <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/>
301 </collection> 314 </collection>
315 <data name="run_info" label="IRMA run info" format="txt" from_work_dir="resultDir/logs/run_info.txt">
316 <filter>optional_outputs and 'run_info' in optional_outputs</filter>
317 </data>
302 </outputs> 318 </outputs>
303 <tests> 319 <tests>
304 <test expect_num_outputs="27"> 320 <test expect_num_outputs="27">
305 <conditional name="input_type_conditional"> 321 <conditional name="input_type_conditional">
306 <param name="fastq_input1" value="test_reads.fq" /> 322 <param name="fastq_input1" value="test_reads.fq" />
452 </element> 468 </element>
453 </output_collection> 469 </output_collection>
454 <output_collection name="bam_collection" type="list" count="8" /> 470 <output_collection name="bam_collection" type="list" count="8" />
455 <output_collection name="vcf_collection" type="list" count="8" /> 471 <output_collection name="vcf_collection" type="list" count="8" />
456 </test> 472 </test>
473 <test expect_num_outputs="19">
474 <conditional name="input_type_conditional">
475 <param name="fastq_input1" value="test_reads.fq" />
476 <param name="input_type" value="single" />
477 </conditional>
478 <conditional name="advanced_config">
479 <param name="customize" value="no" />
480 </conditional>
481 <param name="module" value="FLU-utr" />
482 <param name="optional_outputs" value="amended_consensus,run_info"/>
483 <output_collection name="consensus_collection" type="list">
484 <element name="HA">
485 <assert_contents>
486 <has_n_lines n="2"/>
487 </assert_contents>
488 </element>
489 </output_collection>
490 <output_collection name="amended_collection" type="list">
491 <element name="HA">
492 <assert_contents>
493 <has_n_lines n="2"/>
494 </assert_contents>
495 </element>
496 </output_collection>
497 </test>
457 </tests> 498 </tests>
458 <help><![CDATA[ 499 <help><![CDATA[
459 .. class:: infomark 500 .. class:: infomark
460 501
461 **What it does** 502 **What it does**