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comparison maxbin2.xml @ 6:2bc40bfbcfb4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
author iuc
date Mon, 16 Oct 2023 07:46:13 +0000
parents 8a0473eb465e
children 28a0b1446d2b
comparison
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5:8a0473eb465e 6:2bc40bfbcfb4
1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3"> 1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy4">
2 <description>clusters metagenomic contigs into bins</description> 2 <description>clusters metagenomic contigs into bins</description>
3 <xrefs>
4 <xref type="bio.tools">masigpro</xref>
5 </xrefs>
6 <macros> 3 <macros>
7 <token name="@MAXBIN_VERSION@">2.2.7</token> 4 <token name="@MAXBIN_VERSION@">2.2.7</token>
8 <xml name="contig"> 5 <xml name="contig">
9 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/> 6 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
10 </xml> 7 </xml>
17 <xml name="reads_extra_params"> 14 <xml name="reads_extra_params">
18 <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" /> 15 <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" />
19 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." /> 16 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
20 </xml> 17 </xml>
21 </macros> 18 </macros>
19 <xrefs>
20 <xref type="bio.tools">maxbin</xref>
21 </xrefs>
22 <requirements> 22 <requirements>
23 <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement> 23 <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
24 </requirements> 24 </requirements>
25 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command> 25 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
26 <command detect_errors="exit_code"><![CDATA[ 26 <command detect_errors="exit_code"><![CDATA[
27 ## generate read or abundance files 27 ## generate read or abundance files
28 #import re
28 #if $assembly.inputs.type == 'reads' 29 #if $assembly.inputs.type == 'reads'
29 #if $assembly.type == 'individual' 30 #if $assembly.type == 'individual'
30 echo '$assembly.inputs.reads' >> reads_list && 31 ## uncompress .gz reads files if necessary
32 #set $e = $assembly.inputs.reads
33 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
34 #if $e.ext.endswith(".gz")
35 gunzip -c '$e' > '$identifier' &&
36 echo '$identifier' >> reads_list &&
37 #else
38 ln -s '$e' '$identifier' &&
39 echo '$identifier' >> reads_list &&
40 #end if
31 #else 41 #else
32 #for $r in $assembly.inputs.reads 42 #for $i, $r in enumerate($assembly.inputs.reads)
33 #if $r 43 #if $r
34 echo '$r' >> reads_list && 44 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($r.element_identifier))
45 #set $newid = $identifier + '_' + str($i)
46 #if $r.ext.endswith(".gz")
47 gunzip -c '$r' > '$newid' &&
48 echo '$newid' >> reads_list &&
49 #else
50 ln -s '$r' '$newid' &&
51 echo '$newid' >> reads_list &&
52 #end if
35 #end if 53 #end if
36 #end for 54 #end for
37 #end if 55 #end if
38 #else if $assembly.inputs.type == 'abund' 56 #else if $assembly.inputs.type == 'abund'
39 #if $assembly.type == 'individual' 57 #if $assembly.type == 'individual'
92 </param> 110 </param>
93 <when value="individual"> 111 <when value="individual">
94 <conditional name="inputs"> 112 <conditional name="inputs">
95 <expand macro="input_type"/> 113 <expand macro="input_type"/>
96 <when value="reads"> 114 <when value="reads">
97 <param argument="-reads" type="data" format="fasta,fastq" label="Reads file"/> 115 <param argument="-reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Reads file"/>
98 <expand macro="reads_extra_params"/> 116 <expand macro="reads_extra_params"/>
99 </when> 117 </when>
100 <when value="abund"> 118 <when value="abund">
101 <param argument="-abund" type="data" format="tabular" label="Abundance file"/> 119 <param argument="-abund" type="data" format="tabular" label="Abundance file"/>
102 </when> 120 </when>
342 <has_text text="out.002.fasta"/> 360 <has_text text="out.002.fasta"/>
343 <has_text text="2878"/> 361 <has_text text="2878"/>
344 </assert_contents> 362 </assert_contents>
345 </output> 363 </output>
346 </test> 364 </test>
365 <!-- test w contigs and reads in fastqsanger format as input -->
366 <test expect_num_outputs="4">
367 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
368 <conditional name="assembly">
369 <param name="type" value="individual"/>
370 <conditional name="inputs">
371 <param name="type" value="reads"/>
372 <param name="reads" value="test4_reads.fastqsanger" ftype="fastqsanger"/>
373 <param name="output_abundances" value="false"/>
374 <param name="reassembly" value=""/>
375 </conditional>
376 </conditional>
377 <section name="adv">
378 <param name="min_contig_length" value="1000"/>
379 <param name="max_iteration" value="50"/>
380 <param name="prob_threshold" value="0.5"/>
381 </section>
382 <section name="output">
383 <param name="plotmarker" value=""/>
384 <param name="marker" value="false"/>
385 <param name="markers" value="false" />
386 <param name="log" value="false"/>
387 <param name="markerset" value="107"/>
388 </section>
389 <output_collection name="bins" type="list" count="2">
390 <element name="001" file="4/out.001.fasta" ftype="fasta"/>
391 <element name="002" file="4/out.002.fasta" ftype="fasta"/>
392 </output_collection>
393 <output name="summary" file="4/out.summary" ftype="tabular" />
394 <output name="noclass" file="4/out.noclass" ftype="fasta" />
395 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
396 </test>
397 <!-- test w contigs and reads in fastqsanger.gz format as input -->
398 <test expect_num_outputs="4">
399 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
400 <conditional name="assembly">
401 <param name="type" value="individual"/>
402 <conditional name="inputs">
403 <param name="type" value="reads"/>
404 <param name="reads" value="test4_reads.fastqsanger.gz" ftype="fastqsanger.gz"/>
405 <param name="output_abundances" value="false"/>
406 <param name="reassembly" value=""/>
407 </conditional>
408 </conditional>
409 <section name="adv">
410 <param name="min_contig_length" value="1000"/>
411 <param name="max_iteration" value="50"/>
412 <param name="prob_threshold" value="0.5"/>
413 </section>
414 <section name="output">
415 <param name="plotmarker" value=""/>
416 <param name="marker" value="false"/>
417 <param name="markers" value="false" />
418 <param name="log" value="false"/>
419 <param name="markerset" value="107"/>
420 </section>
421 <output_collection name="bins" type="list" count="2">
422 <element name="001" file="4/out.001.fasta" ftype="fasta"/>
423 <element name="002" file="4/out.002.fasta" ftype="fasta"/>
424 </output_collection>
425 <output name="summary" file="4/out.summary" ftype="tabular" />
426 <output name="noclass" file="4/out.noclass" ftype="fasta" />
427 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
428 </test>
429 <!-- test w co-assembled contigs and multiple reads as .gz and optional outputs -->
430 <test expect_num_outputs="9">
431 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
432 <conditional name="assembly">
433 <param name="type" value="coassembly"/>
434 <conditional name="inputs">
435 <param name="type" value="reads"/>
436 <param name="reads" value="test4_reads.fastqsanger.gz,test4_reads.fastqsanger.gz" ftype="fasta"/>
437 <param name="output_abundances" value="true"/>
438 <param name="reassembly" value=""/>
439 </conditional>
440 </conditional>
441 <section name="adv">
442 <param name="min_contig_length" value="1000"/>
443 <param name="max_iteration" value="50"/>
444 <param name="prob_threshold" value="0.5"/>
445 </section>
446 <section name="output">
447 <param name="plotmarker" value="true"/>
448 <param name="marker" value="true"/>
449 <param name="markers" value="true" />
450 <param name="log" value="true"/>
451 <param name="markerset" value="107"/>
452 </section>
453 <output_collection name="bins" type="list" count="2">
454 <element name="001" file="4/out.001.fasta" ftype="fasta"/>
455 <element name="002" file="4/out.002.fasta" ftype="fasta"/>
456 </output_collection>
457 <output name="summary" ftype="tabular">
458 <assert_contents>
459 <has_text text="Completeness"/>
460 <has_text text="out.001.fasta"/>
461 </assert_contents>
462 </output>
463 <output name="noclass" file="4/out.noclass" ftype="fasta" />
464 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
465 <output name="log" ftype="txt" >
466 <assert_contents>
467 <has_text text="Input contig"/>
468 <has_text text="Elapsed time"/>
469 <has_text text="Yielded 2 bins for contig (scaffold) file"/>
470 </assert_contents>
471 </output>
472 <output name="abundout" file="4/out.abund1" ftype="tabular" />
473 <output name="marker" file="4/out.marker" ftype="tabular" />
474 <output name="plot" file="4/out.marker.pdf" ftype="pdf" compare="sim_size" />
475 <output_collection name="markers" type="list" count="2">
476 <element name="001" ftype="fasta">
477 <assert_contents>
478 <has_text text=">out.001.Methyltransf_5"/>
479 </assert_contents>
480 </element>
481 <element name="002" ftype="fasta">
482 <assert_contents>
483 <has_text text=">out.002.Methyltransf_5"/>
484 </assert_contents>
485 </element>
486 </output_collection>
487 </test>
347 </tests> 488 </tests>
348 <help><![CDATA[ 489 <help><![CDATA[
349 MaxBin is a software that clusters metagenomic contigs into different bins, 490 MaxBin is a software that clusters metagenomic contigs into different bins,
350 each consists (hopefully) of contigs from one species. MaxBin uses the 491 each consists (hopefully) of contigs from one species. MaxBin uses the
351 nucleotide composition information and contig abundance information to do 492 nucleotide composition information and contig abundance information to do