comparison unicycler.xml @ 11:8f9f06995f98 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
author iuc
date Tue, 19 Dec 2023 15:58:30 +0000
parents d10bdad2fd17
children 3e44ef016b45
comparison
equal deleted inserted replaced
10:d10bdad2fd17 11:8f9f06995f98
2 <description>pipeline for bacterial genomes</description> 2 <description>pipeline for bacterial genomes</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.5.0</token> 4 <token name="@TOOL_VERSION@">0.5.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <xrefs>
8 <xref type="bio.tools">unicycler</xref>
9 </xrefs>
10 <edam_topics> 7 <edam_topics>
11 <edam_topic>topic_0196</edam_topic> 8 <edam_topic>topic_0196</edam_topic>
12 </edam_topics> 9 </edam_topics>
13 <edam_operations> 10 <edam_operations>
14 <edam_operation>operation_0525</edam_operation> 11 <edam_operation>operation_0525</edam_operation>
15 </edam_operations> 12 </edam_operations>
13 <xrefs>
14 <xref type="bio.tools">unicycler</xref>
15 </xrefs>
16 <requirements> 16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement>
18 <requirement type="package" version="1.15.1">samtools</requirement> 18 <requirement type="package" version="1.15.1">samtools</requirement>
19 </requirements> 19 </requirements>
20 <command detect_errors="exit_code"><![CDATA[ 20 <command detect_errors="exit_code"><![CDATA[
21 #for r in $reuse
22 ln -s $r.reuse_file ${r.reuse_step}.gfa &&
23 #end for
24
21 ## Preparing files 25 ## Preparing files
22 #set $uncompressed = ('fastqsanger','fastq') 26 #set $uncompressed = ('fastqsanger','fastq')
23 #set $compressed = ('fastqsanger.gz','fastq.gz') 27 #set $compressed = ('fastqsanger.gz','fastq.gz')
24 #if str( $paired_unpaired.fastq_input_selector ) == "paired" 28 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
25 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed 29 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
206 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1"> 210 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1">
207 <option value="0">0: only keep final files</option> 211 <option value="0">0: only keep final files</option>
208 <option value="1" selected="true">1: save graphs at main checkpoints</option> 212 <option value="1" selected="true">1: save graphs at main checkpoints</option>
209 <option value="2">2: also keep SAM</option> 213 <option value="2">2: also keep SAM</option>
210 </param> 214 </param>
215 <repeat name="reuse" title="Reuse checkpoint files from earlier runs" max="1" help="">
216 <param name="reuse_file" type="data" optional="false" format="gfa1" label="Checkpoint file"/>
217 <param name="reuse_step" type="select" label="Checkpoint">
218 <option value="002_depth_filter">002_depth_filter</option>
219 <option value="003_overlaps_removed">003_overlaps_removed</option>
220 <option value="004_bridges_applied">004_bridges_applied</option>
221 </param>
222 </repeat>
211 </inputs> 223 </inputs>
212 <outputs> 224 <outputs>
213 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> 225 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
214 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> 226 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
215 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs"> 227 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs">
216 <discover_datasets pattern="__designation_and_ext__" format="gfa1" directory="spades_graphs"/> 228 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gfa" format="gfa1" directory="spades_graphs"/>
217 <filter>keep != "0"</filter> 229 <filter>keep != "0"</filter>
218 </collection> 230 </collection>
219 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM"> 231 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM">
220 <filter>keep == "2" and long</filter> 232 <filter>keep == "2" and long</filter>
221 </data> 233 </data>
373 <assert_contents> 385 <assert_contents>
374 <has_text text=">1" /> 386 <has_text text=">1" />
375 </assert_contents> 387 </assert_contents>
376 </output> 388 </output>
377 </test> 389 </test>
390 <!-- test checkpoint graph reuse
391 TODO more precise test and check difference to call wo reuse -->
392 <test expect_num_outputs="2">
393 <conditional name="paired_unpaired">
394 <param name="fastq_input_selector" value="paired_collection"/>
395 <param name="fastq_input1">
396 <collection type="paired">
397 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
398 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
399 </collection>
400 </param>
401 </conditional>
402 <param name="long" value="only_long.fasta" ftype="fasta" />
403 <repeat name="reuse">
404 <param name="reuse_file" value="phix__spades_graph.gfa1"/>
405 <param name="reuse_step" value="002_depth_filter"/>
406 </repeat>
407 <param name="keep" value="0"/>
408 <output name="assembly_graph" ftype="gfa1">
409 <assert_contents>
410 <has_text text="S" />
411 </assert_contents>
412 </output>
413 <output name="assembly" ftype="fasta">
414 <assert_contents>
415 <has_text text=">1" />
416 </assert_contents>
417 </output>
418 </test>
378 <!-- Test keep value = 1 --> 419 <!-- Test keep value = 1 -->
379 <test expect_num_outputs="3"> 420 <test expect_num_outputs="3">
380 <conditional name="paired_unpaired"> 421 <conditional name="paired_unpaired">
381 <param name="fastq_input_selector" value="paired" /> 422 <param name="fastq_input_selector" value="paired" />
382 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> 423 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
426 <element name="001_spades_graph_k027"> 467 <element name="001_spades_graph_k027">
427 <assert_contents> 468 <assert_contents>
428 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> 469 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/>
429 </assert_contents> 470 </assert_contents>
430 </element> 471 </element>
472 <!-- there are gfa files for more k that are not tested explicily
473 Aim of testing these is to be sure about the names of the graphs,
474 since they are used for reuse. Hence if there is a change here
475 update reuse accordingly-->
476 <element name="001_spades_graph_k127">
477 <assert_contents>
478 <has_line_matching expression="^S.*"/>
479 </assert_contents>
480 </element>
481 <element name="002_depth_filter">
482 <assert_contents>
483 <has_line_matching expression="^S.*"/>
484 </assert_contents>
485 </element>
486 <element name="003_overlaps_removed">
487 <assert_contents>
488 <has_line_matching expression="^S.*"/>
489 </assert_contents>
490 </element>
491 <element name="004_bridges_applied">
492 <assert_contents>
493 <has_line_matching expression="^S.*"/>
494 </assert_contents>
495 </element>
496 <element name="005_final_clean">
497 <assert_contents>
498 <has_line_matching expression="^S.*"/>
499 </assert_contents>
500 </element>
431 </output_collection> 501 </output_collection>
432 <output name="bam_file" ftype="bam"> 502 <output name="bam_file" ftype="bam">
433 <assert_contents> 503 <assert_contents>
434 <has_size value="2084" delta="100"/> 504 <has_size value="2084" delta="100"/>
435 </assert_contents> 505 </assert_contents>