Mercurial > repos > iuc > orfipy

changeset 2:f5114c60dc95 draft default tip

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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
files macros.xml orfipy.xml
diffstat 2 files changed, 43 insertions(+), 70 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>