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Changeset 2:f5114c60dc95 (2024-06-04)

Previous changeset 1:45d4d26e01b5 (2022-09-22)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed

modified:
macros.xml
orfipy.xml

diff -r 45d4d26e01b5 -r f5114c60dc95 macros.xml
--- a/macros.xml Thu Sep 22 14:03:42 2022 +0000
+++ b/macros.xml Tue Jun 04 10:56:16 2024 +0000

@@ -1,6 +1,6 @@
<macros>
     <token name="@TOOL_VERSION@">0.0.4</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="xrefs">
         <xrefs>
             <xref type="bio.tools">orfipy</xref>

diff -r 45d4d26e01b5 -r f5114c60dc95 orfipy.xml
--- a/orfipy.xml Thu Sep 22 14:03:42 2022 +0000
+++ b/orfipy.xml Tue Jun 04 10:56:16 2024 +0000

[

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