Mercurial > repos > iuc > binning_refiner

comparison binning_refiner.xml @ 1:1c8d0916f97f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
author iuc
date Wed, 27 Apr 2022 18:46:46 +0000
parents f350d182f786
children 1b18b36bad5e
comparison
equal deleted inserted replaced
0:f350d182f786 1:1c8d0916f97f
28 #end for 28 #end for
29 29
30 Binning_refiner 30 Binning_refiner
31 -i input_bin_dir 31 -i input_bin_dir
32 -p 'refined' 32 -p 'refined'
33 -m $m
33 && mv 'refined_Binning_refiner_outputs/refined_contigs.txt' '$output_refined_contigs' 34 && mv 'refined_Binning_refiner_outputs/refined_contigs.txt' '$output_refined_contigs'
34 && mv 'refined_Binning_refiner_outputs/refined_sources_and_length.txt' '$output_sources_and_length' 35 && mv 'refined_Binning_refiner_outputs/refined_sources_and_length.txt' '$output_sources_and_length'
35 ]]></command> 36 ]]></command>
36 <inputs> 37 <inputs>
37 <param name="input_bins" format="fasta,fasta.gz" type="data" multiple="true" label="Binned fasta files"/> 38 <param name="input_bins" format="fasta,fasta.gz" type="data" multiple="true" label="Binned fasta files"/>
45 <data name="output_sources_and_length" format="tabular" label="${tool.name} on ${on_string} (sources and length)"/> 46 <data name="output_sources_and_length" format="tabular" label="${tool.name} on ${on_string} (sources and length)"/>
46 </outputs> 47 </outputs>
47 <tests> 48 <tests>
48 <test expect_num_outputs="3"> 49 <test expect_num_outputs="3">
49 <param name="input_bins" value="MetaBAT_17.fa.gz,MetaBAT_18.fa.gz,MetaBAT_19.fa.gz,MetaBAT_20.fa.gz,MetaBAT_21.fa.gz,MetaBAT_22.fa.gz,MetaBAT_23.fa.gz,Concoct_1.fa.gz,Concoct_3.fa.gz,Concoct_8.fa.gz" ftype="fasta.gz"/> 50 <param name="input_bins" value="MetaBAT_17.fa.gz,MetaBAT_18.fa.gz,MetaBAT_19.fa.gz,MetaBAT_20.fa.gz,MetaBAT_21.fa.gz,MetaBAT_22.fa.gz,MetaBAT_23.fa.gz,Concoct_1.fa.gz,Concoct_3.fa.gz,Concoct_8.fa.gz" ftype="fasta.gz"/>
50 <output_collection name="output_refined_bins" type="list" count="7"> 51 <param name="m" value="256"/>
52 <output_collection name="output_refined_bins" type="list" count="8">
51 <element name="refined_1" ftype="fasta"> 53 <element name="refined_1" ftype="fasta">
52 <assert_contents> 54 <assert_contents>
53 <has_size value="1320640"/> 55 <has_size value="1320640"/>
54 <has_text text=">scaffold_2064"/> 56 <has_text text=">scaffold_2064"/>
55 <has_n_lines n="21765"/> 57 <has_n_lines n="21765"/>
95 <has_size value="560996"/> 97 <has_size value="560996"/>
96 <has_text text=">scaffold_1510"/> 98 <has_text text=">scaffold_1510"/>
97 <has_n_lines n="9219"/> 99 <has_n_lines n="9219"/>
98 </assert_contents> 100 </assert_contents>
99 </element> 101 </element>
102 <element name="refined_8" ftype="fasta">
103 <assert_contents>
104 <has_size value="276224"/>
105 <has_text text=">scaffold_955"/>
106 <has_n_lines n="4554"/>
107 </assert_contents>
108 </element>
100 </output_collection> 109 </output_collection>
101 <output name="output_refined_contigs" file="output_refined_contigs.tabular" ftype="tabular"/> 110 <output name="output_refined_contigs" file="output_refined_contigs.tabular" ftype="tabular"/>
102 <output name="output_sources_and_length" file="output_sources_and_length.tabular" ftype="tabular"/> 111 <output name="output_sources_and_length" file="output_sources_and_length.tabular" ftype="tabular"/>
103 </test> 112 </test>
104 </tests> 113 </tests>