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comparison maxbin2.xml @ 7:28a0b1446d2b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit be3f3d0eb7e565cea414babb410e6ae32875c5f2
author iuc
date Wed, 20 Dec 2023 20:27:57 +0000
parents 2bc40bfbcfb4
children 9da9706f7ca9
comparison
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6:2bc40bfbcfb4 7:28a0b1446d2b
1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy4"> 1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy5">
2 <description>clusters metagenomic contigs into bins</description> 2 <description>clusters metagenomic contigs into bins</description>
3 <macros> 3 <macros>
4 <token name="@MAXBIN_VERSION@">2.2.7</token> 4 <token name="@MAXBIN_VERSION@">2.2.7</token>
5 <xml name="contig"> 5 <xml name="contig">
6 <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"/>
28 #import re 28 #import re
29 #if $assembly.inputs.type == 'reads' 29 #if $assembly.inputs.type == 'reads'
30 #if $assembly.type == 'individual' 30 #if $assembly.type == 'individual'
31 ## uncompress .gz reads files if necessary 31 ## uncompress .gz reads files if necessary
32 #set $e = $assembly.inputs.reads 32 #set $e = $assembly.inputs.reads
33 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) 33 #set $identifier = re.sub('[^\w\-\\.]', '_', str($e.element_identifier))
34 #if $e.ext.endswith(".gz") 34 #if $e.ext.endswith(".gz")
35 gunzip -c '$e' > '$identifier' && 35 gunzip -c '$e' > '$identifier' &&
36 echo '$identifier' >> reads_list && 36 echo '$identifier' >> reads_list &&
37 #else 37 #else
38 ln -s '$e' '$identifier' && 38 ln -s '$e' '$identifier' &&
392 </output_collection> 392 </output_collection>
393 <output name="summary" file="4/out.summary" ftype="tabular" /> 393 <output name="summary" file="4/out.summary" ftype="tabular" />
394 <output name="noclass" file="4/out.noclass" ftype="fasta" /> 394 <output name="noclass" file="4/out.noclass" ftype="fasta" />
395 <output name="toshort" file="4/out.tooshort" ftype="fasta" /> 395 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
396 </test> 396 </test>
397 <!-- test w contigs and reads in fastqsanger format as input (and whitespace in reads filename)-->
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 2.fastqsanger" ftype="fastqsanger"/>
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>
397 <!-- test w contigs and reads in fastqsanger.gz format as input --> 429 <!-- test w contigs and reads in fastqsanger.gz format as input -->
398 <test expect_num_outputs="4"> 430 <test expect_num_outputs="4">
399 <param name="contig" value="test4_contigs.fasta" ftype="fasta" /> 431 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
400 <conditional name="assembly"> 432 <conditional name="assembly">
401 <param name="type" value="individual"/> 433 <param name="type" value="individual"/>