Mercurial > repos > mbernt > maxbin2
comparison maxbin2.xml @ 7:28a0b1446d2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit be3f3d0eb7e565cea414babb410e6ae32875c5f2
author | iuc |
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date | Wed, 20 Dec 2023 20:27:57 +0000 |
parents | 2bc40bfbcfb4 |
children | 9da9706f7ca9 |
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6:2bc40bfbcfb4 | 7:28a0b1446d2b |
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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"/> |