Mercurial > repos > iuc > orfipy
diff orfipy.xml @ 2:f5114c60dc95 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
| author | iuc |
|---|---|
| date | Tue, 04 Jun 2024 10:56:16 +0000 |
| parents | 45d4d26e01b5 |
| children |
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--- a/orfipy.xml Thu Sep 22 14:03:42 2022 +0000 +++ b/orfipy.xml Tue Jun 04 10:56:16 2024 +0000 @@ -11,19 +11,21 @@ orfipy --procs "\${GALAXY_SLOTS:-1}" --outdir ./ -#for $o in str($out_files).split(','): - #if $o == 'BED': - --bed '$out_bed' - #else if $o == 'BED12': - --bed12 '$out_bed12' - #else if $o == 'DNA': - --dna '$out_dna' - #else if $o == 'RNA': - --rna '$out_rna' - #else if $o == 'PEP': - --pep '$out_pep' - #end if -#end for +#if 'BED' in $out_files or $longest: + --bed '$out_bed' +#end if +#if 'BED12' in $out_files: + --bed12 '$out_bed12' +#end if +#if 'DNA' in $out_files: + --dna '$out_dna' +#end if +#if 'RNA' in $out_files: + --rna '$out_rna' +#end if +#if 'PEP' in $out_files: + --pep '$out_pep' +#end if --strand $strand #if $min: --min $min @@ -43,11 +45,12 @@ $partial_5 $between_stops $include_stop +$longest '$input1' ]]></command> <inputs> <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/> - <param type="select" argument="--table" label="Specify genetic code"> + <param argument="--table" type="select" label="Specify genetic code"> <option value="1" selected="true">1 Standard</option> <option value="2">2 Vertebrate mitochondrial</option> <option value="3">3 Yeast mitochondrial</option> @@ -72,15 +75,14 @@ <option value="22">22 Mesodinium nuclear</option> <option value="23">23 Peritrich nuclear</option> </param> - <param name="out_files" argument="--bed,--bed12,--dna,--rna,--pep" type="select" multiple="true" display="checkboxes" label="Select outputs" - help="DNA, RNA, and Peptide options will produce FASTA outputs"> + <param name="out_files" type="select" label="Select outputs" help="DNA, RNA, and Peptide options will produce FASTA outputs" multiple="true" display="checkboxes"> <option value="BED" selected="true">BED</option> <option value="BED12">BED12</option> <option value="DNA">DNA</option> <option value="RNA">RNA</option> <option value="PEP">Peptides</option> </param> - <param argument="--strand" type="select" display="radio" label="Select strand" help="Identify ORFs on which strand"> + <param argument="--strand" type="select" label="Select strand" help="Identify ORFs on which strand" display="radio"> <option value="b" selected="true">Both</option> <option value="f">Forward</option> <option value="r">Reverse</option> @@ -97,20 +99,16 @@ help="A commma separated list without spaces. Only ATCG and comma are allowed"> <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator> </param> - <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" display="radio" label="Ignore case?" - help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore"/> - <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" display="radio" label="Output ORFs with Start but no Stop?" - help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output"/> - <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" display="radio" label="Output ORFs with Stop but no Start?" - help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output"/> - <param argument="--between-stops" type="boolean" display="radio" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?" - help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true"/> - <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" display="radio" label="Include stop codon in the results?" - help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include"/> + <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" label="Ignore case?" help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore" display="radio"/> + <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" label="Output ORFs with Start but no Stop?" help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output" display="radio"/> + <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" label="Output ORFs with Stop but no Start?" help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output" display="radio"/> + <param argument="--between-stops" type="boolean" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?" help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true" display="radio"/> + <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" label="Include stop codon in the results?" help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include" display="radio"/> + <param argument="--longest" type="boolean" truevalue="--longest" falsevalue="" label="Output separate BED file with longest ORFs per sequence" help="Setting this option will automatically enable the BED option."/> </inputs> <outputs> <data name="out_bed" format="bed6" label="ORFs on ${on_string} (BED format)"> - <filter>"BED" in out_files</filter> + <filter>"BED" in out_files or longest</filter> </data> <data name="out_bed12" format="bed12" label="ORFs on ${on_string} (BED12 format)"> <filter>"BED12" in out_files</filter> @@ -151,52 +149,27 @@ <param name="max" value="100000000"/> <output name="out_dna" file="test3.fa"/> </test> + <test expect_num_outputs="2"> + <param name="input1" value="orfipy.fa.gz"/> + <param name="out_files" value="DNA"/> + <param name="max" value="100000000"/> + <param name="longest" value="true"/> + <output name="out_dna" file="test3.fa"/> + <output name="out_bed" file="test1.bed"/> + </test> + <test expect_num_outputs="1"> + <param name="input1" value="orfipy.fa"/> + <param name="out_files" value="BED"/> + <param name="longest" value="true"/> + <output name="out_bed" file="test1.bed"/> + </test> </tests> <help><![CDATA[ **What it does** -Orfipy is a tool for finding open reading frames (ORFs). - -**Parameters** +Orfipy is a tool for finding open reading frames (ORFs) in sequences (FASTA files). -Galaxy interface of Orfipy supports the following parameters (the following is taken from the tool help):: - - --table TABLE The codon table number to use or path to .json file - with codon table. Use --show-tables to see available - tables compiled from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes Default: 1 - --start START Comma-separated list of start-codons. This will - override start codons described in translation table. - E.g. "--start ATG,ATT" Default: Derived from the - translation table selected - --stop STOP Comma-separated list of stop codons. This will - override stop codons described in translation table. - E.g. "--start TAG,TTT" Default: Derived from the - translation table selected - --outdir OUTDIR Path to outdir default: orfipy_<infasta>_out - --bed12 BED12 bed12 out file Default: None - --bed BED bed out file Default: None - --dna DNA fasta (DNA) out file Default: None - --rna RNA fasta (RNA) out file Default: None - --pep PEP fasta (peptide) out file Default: None - --min MIN Minimum length of ORF, excluding stop codon - (nucleotide) Default: 30 - --max MAX Maximum length of ORF, excluding stop codon - (nucleotide) Default: 1,000,000,000 - --strand {f,r,b} Strands to find ORFs [(f)orward,(r)everse,(b)oth] - Default: b - --ignore-case Ignore case and find ORFs in lower case sequences too. - Useful for soft-masked sequences. Default: False - --partial-3 Output ORFs with a start codon but lacking an inframe - stop codon. E.g. "ATG TTT AAA" Default: False - --partial-5 Output ORFs with an inframe stop codon lacking an - inframe start codon. E.g. "TTT AAA TAG" Default: False - --between-stops Output ORFs defined as regions between stop codons - (regions free of stop codon). This will set - --partial-3 and --partial-5 true. Default: False - --include-stop Include stop codon in the results, if a stop codon - exists. This output format is compatible with - TransDecoder's which includes stop codon coordinates - Default: False + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btab090</citation>