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comparison metawrapmg_binning.xml @ 3:6f7211f93b06 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg commit 0f381ce2cdb0683f1bc8e1da321a5a75440bf619
author iuc
date Tue, 11 Mar 2025 12:23:05 +0000
parents 2a8bc1d26d06
children
comparison
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2:2a8bc1d26d06 3:6f7211f93b06
14 ################## 14 ##################
15 ## SET UP FILES ## 15 ## SET UP FILES ##
16 ################## 16 ##################
17 17
18 ## only plain FASTA and FASTQ 18 ## only plain FASTA and FASTQ
19 ln -s '$metagenome' metagenome.fasta 19 ln -s '$metagenome' metagenome.fasta &&
20 &&
21 ## Metawrap checks for files named _1.fastq and _2.fastq. 20 ## Metawrap checks for files named _1.fastq and _2.fastq.
22 ln -s '$input_1' reads_1.fastq 21 ln -s '$input.forward' reads_1.fastq &&
23 && 22 ln -s '$input.reverse' reads_2.fastq &&
24 ln -s '$input_2' reads_2.fastq
25 &&
26 23
27 ##################### 24 #####################
28 ## INITIAL BINNING ## 25 ## INITIAL BINNING ##
29 ##################### 26 #####################
30 27
69 ## Only run bin_refinement on bins with contigs 66 ## Only run bin_refinement on bins with contigs
70 "\${bin_string}" 67 "\${bin_string}"
71 ]]></command> 68 ]]></command>
72 <inputs> 69 <inputs>
73 <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/> 70 <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/>
74 <param name="input_1" format="fastqsanger" type="data" label="Read 1" help="Original reads that were used for the assembly: read 1."/> 71 <param name="input" type="data_collection" collection_type="paired" label="Reads" help="Original reads that were used for the assembly"/>
75 <param name="input_2" format="fastqsanger" type="data" label="Read 2" help="Original reads that were used for the assembly: read 2."/>
76 <section name="binning" title="Binning parameters" expanded="false"> 72 <section name="binning" title="Binning parameters" expanded="false">
77 <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/> 73 <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/>
78 <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/> 74 <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/>
79 </section> 75 </section>
80 <!-- the pplacer component requires 40 GB per thread. Skip pplacer for 76 <!-- the pplacer component requires 40 GB per thread. Skip pplacer for
101 </outputs> 97 </outputs>
102 <tests> 98 <tests>
103 <!-- 01: basic function --> 99 <!-- 01: basic function -->
104 <test> 100 <test>
105 <param name="metagenome" value="subset.fasta.gz"/> 101 <param name="metagenome" value="subset.fasta.gz"/>
106 <param name="input_1" value="mapped_reads.r1.fastq.gz"/> 102 <param name="input">
107 <param name="input_2" value="mapped_reads.r2.fastq.gz"/> 103 <collection type="paired">
108 <param name="c" value="60"/> 104 <element name="forward" value="mapped_reads.r1.fastq.gz"/>
109 <param name="x" value="15"/> 105 <element name="reverse" value="mapped_reads.r2.fastq.gz"/>
106 </collection>
107 </param>
108 <section name="binning">
109 <param name="c" value="60"/>
110 <param name="x" value="15"/>
111 </section>
110 <param name="hidden_quick" value="--quick"/> 112 <param name="hidden_quick" value="--quick"/>
111 <output_collection name="metawrap_bins" type="list"> 113 <output_collection name="metawrap_bins" type="list">
112 <element name="bin.1" ftype="fasta"> 114 <element name="bin.1" ftype="fasta">
113 <assert_contents> 115 <assert_contents>
114 <has_text text="NODE_2_length_"/> 116 <has_text text="NODE_2_length_"/>