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author | galaxyp |
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date | Wed, 21 Mar 2018 17:15:25 -0400 |
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children | 17c7ab82bfbc |
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<tool id="metagene_annotator" name="MetaGeneAnnotator" version="1.0.0"> <description>gene-finding program for prokaryote and phage (used by sixgill)</description> <requirements> <requirement type="package">metagene_annotator</requirement> <requirement type="package">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #set $output_list = str($output_formats).split(',') touch mga_output #for $input in $inputs: && mga ${input} $multiple_species >> mga_output #end for #if 'tsv' in $output_list or 'bed' in $output_list: && python '$__tool_directory__/convert_mga.py' mga_output -v #if 'tsv' in $output_list --tsv '$mga_tsv' #end if #if 'bed' in $output_list --bed '$mga_bed' #end if #end if ]]></command> <inputs> <param name="inputs" type="data" format="fasta" multiple="true" label="prokaryote DNA sequences"/> <param name="multiple_species" type="boolean" truevalue="-m" falsevalue="-s" checked="true" label="MetaGenomic - Sequences are from multiple organisms" /> <param name="output_formats" type="select" multiple="true" display="checkboxes" label="output formats"> <option value="txt" selected="true">MetaGeneAnnotator text report</option> <option value="tsv">MetaGeneAnnotator tabular report with sequence columns</option> <option value="bed">MetaGeneAnnotator in BED format</option> </param> </inputs> <outputs> <data name="mga_txt" format="txt" from_work_dir="mga_output" label="${tool.name} on ${on_string} metagenefile"> <filter>'txt' in output_formats</filter> </data> <data name="mga_tsv" format="tabular" label="${tool.name} on ${on_string} mga table"> <filter>'tsv' in output_formats</filter> <actions> <action name="column_names" type="metadata" default="seq_ID,seq_model,seq_gc,seq_rbs,gene ID,start pos,end pos,strand,frame,complete/partial,gene score,used model,rbs start,rbs end,rbs score"/> </actions> </data> <data name="mga_bed" format="bed" label="${tool.name} on ${on_string} mga bed"> <filter>'bed' in output_formats</filter> <actions> <action name="column_names" type="metadata" default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/> </actions> </data> </outputs> <tests> <test> <param name="inputs" value="metasequences.fasta" ftype="fasta"/> <param name="multiple_species" value="True"/> <param name="output_formats" value="txt"/> <output name="mga_txt"> <assert_contents> <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" /> <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> </assert_contents> </output> </test> <test> <param name="inputs" value="metasequences.fasta" ftype="fasta"/> <param name="multiple_species" value="False"/> <param name="output_formats" value="txt"/> <output name="mga_txt"> <assert_contents> <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = 0.428571\s# self: b" /> <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t12.48\d+\tb\t2002\t2007\t0.49\d+" /> </assert_contents> </output> </test> <!-- Try these later <test> <param name="inputs" value="metasequences1.fasta,metasequences2.fasta" ftype="fasta"/> <param name="multiple_species" value="True"/> <param name="output_formats" value="txt"/> <output name="mga_txt"> <assert_contents> <has_text_matching expression="# 1/1.*# 10/1" /> <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> </assert_contents> </output> </test> <test> <param name="inputs" value="metasequences.fasta" ftype="fasta"/> <param name="multiple_species" value="True"/> <param name="output_formats" value="txt,tsv,bed"/> <output name="mga_txt"> <assert_contents> <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" /> <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> </assert_contents> </output> <output name="mga_tsv"> <assert_contents> <has_text_matching expression="#seq_id\tseq_model\tseq_gc\tseq_rbs" /> <has_text_matching expression="1/1\t-\t0.27\d+\t-1\tgene_1\t1812\t1994\t-\t0\t11\t14.1035\tb\t2002\t2007\t2.11\d+" /> </assert_contents> </output> <output name="mga_bed"> <assert_contents> <has_text_matching expression="1/1\t1811\t1994\t1/1:gene_1\t15\t-\t1811\t1994\t0\t1\t183\t0" /> </assert_contents> </output> </test> --> </tests> <help><![CDATA[ **MetaGeneAnnotator (mga)** A gene-finding program for prokaryote and phage. The gene annotations can be used by sixgill_ when generating metapeptides from metagenomics shotgun sequencing. .. image:: Sixgill_MetaGeneAnnotator_Workflow.png :height: 213 :width: 625 usage: mga [multi-fasta] <-m/-s> -m (multiple species sequences are individually treated) -s (single species sequences are treated as a unit) **Input:** *A fasta file of metagenomic sequences* **Outputs:** *MetaGeneAnnotator text report* Output from the MetaGeneAnnotator mga application:: # 1/1 # gc = 0.275862, rbs = -1 # self: - gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797 # 2/1 # gc = 0.338877, rbs = -1 # self: - gene_1 1 414 + 0 01 25.748 b . . . gene_2 614 790 + 0 11 0.774142 b . . . gene_3 822 1079 + 0 11 20.6507 b . . . output format description:: # [sequence name] # gc = [gc%], rbs = [rbs%] # self: [(b)acteria/(a)rchaea/(p)hage/unused(-)] [gene ID] [start pos.] [end pos.] [strand] [frame] [complete/partial] [gene score] [used model] [rbs start] [rbs end] [rbs score] explanations of output column: *The value of [frame] (0/1/2) indicates the number of surplus (untranslated) nucleotides at the 5'-end of the predicted ORF. *The value of [score] indicates the estimated score of predicted gene. All predicted genes are more than 0. *The value of [complete/partial] indicates that the predicted gene structure is whether complete (contains both of start and stop codons[11]) or partial (lacks start[01] or stop[10] or both of them[00]). *The value of [model] indicates a selected model ((s)elf/(b)acteria/(a)rchaea/(p)hage) for predicting the gene. *MetaGeneAnnotator tabular report with sequence columns* The mga output reformated as a tabular file:: #seq_id seq_model seq_gc seq_rbs gene ID start pos end pos strand frame complete/partial gene score used model rbs start rbs end rbs score 1/1 - 0.275862 -1 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797 2/1 - 0.338877 -1 gene_1 1 414 + 0 01 25.748 b . . . 2/1 - 0.338877 -1 gene_2 614 790 + 0 11 0.774142 b . . . 2/1 - 0.338877 -1 gene_3 822 1079 + 0 11 20.6507 b . . . *MetaGeneAnnotator in BED format* The mga output reformatted as a BED file which can be used to extract the DNA sequences for each gene from the fasta file:: 1/1 1811 1994 1/1:gene_1 15 - 1811 1994 0 1 183 0 2/1 0 414 2/1:gene_1 26 + 0 414 0 1 414 0 2/1 613 790 2/1:gene_2 1 + 613 790 0 1 177 0 2/1 821 1079 2/1:gene_3 21 + 821 1079 0 1 258 0 .. _sixgill: https://github.com/dhmay/sixgill ]]></help> <citations> <citation type="doi">10.1093/dnares/dsn027</citation> </citations> </tool>