Repository 'orfipy'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/orfipy

Changeset 1:45d4d26e01b5 (2022-09-22)
Previous changeset 0:c147914c9f02 (2022-05-25) Next changeset 2:f5114c60dc95 (2024-06-04)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
modified:
macros.xml
orfipy.xml
added:
test-data/test3.fa
b
diff -r c147914c9f02 -r 45d4d26e01b5 macros.xml
--- a/macros.xml Wed May 25 14:53:03 2022 +0000
+++ b/macros.xml Thu Sep 22 14:03:42 2022 +0000
b
@@ -1,5 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.0.4</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="xrefs">
         <xrefs>
             <xref type="bio.tools">orfipy</xref>
b
diff -r c147914c9f02 -r 45d4d26e01b5 orfipy.xml
--- a/orfipy.xml Wed May 25 14:53:03 2022 +0000
+++ b/orfipy.xml Thu Sep 22 14:03:42 2022 +0000
[
@@ -1,4 +1,4 @@
-<tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>a versatile ORF finder</description>
     <macros>
         <import>macros.xml</import>
@@ -28,6 +28,9 @@
 #if $min:
     --min $min
 #end if
+#if $max:
+    --max $max
+#end if
 --table $table
 #if $start:
     --start '$start'
@@ -84,6 +87,8 @@
         </param>
         <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
                help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
+        <param argument="--max" type="integer" min="0" optional="true" label="Maximum length of ORFs"
+               help="This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000."/>
         <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
                help="A comma-separated list without spaces. Only ATCG and comma are allowed">
             <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
@@ -140,6 +145,12 @@
             <param name="partial_5" value="true"/>
             <output name="out_dna" file="test2.fa"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="orfipy.fa.gz"/>
+            <param name="out_files" value="DNA"/>
+            <param name="max" value="100000000"/>
+            <output name="out_dna" file="test3.fa"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
b
diff -r c147914c9f02 -r 45d4d26e01b5 test-data/test3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3.fa Thu Sep 22 14:03:42 2022 +0000
[
b'@@ -0,0 +1,755 @@\n+>pbr322_ORF.1 [60-93](+) type:complete length:33 frame:1 start:TTG stop:TAA\n+TTGCTAACGCAGTCAGGCACCGTGTATGAAATC\n+>pbr322_ORF.2 [258-639](+) type:complete length:381 frame:1 start:ATG stop:TAA\n+ATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTT\n+CGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTC\n+TACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATAT\n+CGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCG\n+GCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCA\n+CCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCA\n+GGAGTCGCA\n+>pbr322_ORF.3 [780-1071](+) type:complete length:291 frame:1 start:CTG stop:TGA\n+CTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTG\n+CGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGT\n+TTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCT\n+GGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCA\n+TCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGA\n+>pbr322_ORF.4 [1179-1515](+) type:complete length:336 frame:1 start:ATG stop:TAG\n+ATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGC\n+GTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACG\n+GATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACC\n+AACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTC\n+GGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGC\n+TAGGCTGGCGGGGTTGCCTTACTGGT\n+>pbr322_ORF.5 [1626-1737](+) type:complete length:111 frame:1 start:CTG stop:TGA\n+CTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTG\n+CTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCAT\n+>pbr322_ORF.6 [1881-2103](+) type:complete length:222 frame:1 start:ATG stop:TGA\n+ATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAA\n+CATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACG\n+CGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGC\n+TGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTC\n+>pbr322_ORF.7 [2109-2142](+) type:complete length:33 frame:1 start:ATG stop:TAA\n+ATGCAGCTCCCGGAGACGGTCACAGCTTGTCTG\n+>pbr322_ORF.8 [2214-2283](+) type:complete length:69 frame:1 start:ATG stop:TGA\n+ATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAG\n+ATTGTAC\n+>pbr322_ORF.9 [2370-2430](+) type:complete length:60 frame:1 start:CTG stop:TAA\n+CTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGG\n+>pbr322_ORF.10 [2553-2856](+) type:complete length:303 frame:1 start:CTG stop:TAA\n+CTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAA\n+AGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCT\n+TACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCT\n+GTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCC\n+GTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGG\n+>pbr322_ORF.11 [2889-2919](+) type:complete length:30 frame:1 start:CTG stop:TAG\n+CTGGTAACAGGATTAGCAGAGCGAGGTATG\n+>pbr322_ORF.12 [3027-3132](+) type:complete length:105 frame:1 start:TTG stop:TGA\n+TTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAG\n+CAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTT\n+>pbr322_ORF.13 [3150-3195](+) type:complete length:45 frame:1 start:CTG stop:TGA\n+CTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCA\n+>pbr322_ORF.14 [3270-3303](+) type:complete length:33 frame:1 start:ATG stop:TAA\n+ATGAGTAAACTTGGTCTGACAGTTACCAATGCT\n+>pbr322_ORF.15 [3507-3561](+) type:complete length:54 frame:1 start:CTG stop:TAA\n+CTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAG\n+>pbr322_ORF.16 [3594-3819](+) type:complete length:225 frame:1 start:TTG stop:TAA\n+TTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGC\n+TCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAG\n+CTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA\n+TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCG\n+>pbr322_ORF.17 [3837-3942](+) type:complete length:105 frame:1 start:CTG stop:TAA\n+CTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGC\n+CCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTT\n+>pbr322_ORF.18 [3957-4005](+) type:complete length:48 frame:1 sta'..b'TGCTC\n+>puc18_ORF.92 [3499-4357](-) type:complete length:858 frame:-3 start:ATG stop:TAA\n+ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGT\n+TTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAG\n+TGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAA\n+CGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGA\n+CGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACT\n+CACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCC\n+ATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGA\n+GCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGG\n+AGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACA\n+ACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGA\n+CTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGT\n+TTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGG\n+CCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGA\n+TGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG\n+>puc18_ORF.93 [3466-3496](-) type:complete length:30 frame:-3 start:CTG stop:TAG\n+CTGTCAGACCAAGTTTACTCATATATACTT\n+>puc18_ORF.94 [3169-3310](-) type:complete length:141 frame:-3 start:CTG stop:TAG\n+CTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCC\n+GGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAA\n+ATACTGTCCTTCTAGTG\n+>puc18_ORF.95 [3040-3112](-) type:complete length:72 frame:-3 start:CTG stop:TAG\n+CTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGA\n+CTCAAGACGA\n+>puc18_ORF.96 [2932-2980](-) type:complete length:48 frame:-3 start:TTG stop:TGA\n+TTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTA\n+>puc18_ORF.97 [2623-2707](-) type:complete length:84 frame:-3 start:CTG stop:TGA\n+CTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGA\n+TAACCGTATTACCGCCTTTGAG\n+>puc18_ORF.98 [2365-2404](-) type:complete length:39 frame:-3 start:ATG stop:TAA\n+ATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGA\n+>puc18_ORF.99 [2242-2287](-) type:complete length:45 frame:-3 start:CTG stop:TGA\n+CTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCG\n+>puc18_ORF.100 [1873-1918](-) type:complete length:45 frame:-3 start:ATG stop:TAG\n+ATGTGTGACCTTGCGCCCGGTCTTTCGCTGCGCCCACTCCACCTG\n+>puc18_ORF.101 [1504-1852](-) type:complete length:348 frame:-3 start:CTG stop:TAA\n+CTGCGTCACGGCTGGATCAAGCACTCGCAACTTGAAGTCCTTGATCGAGGGATACCGGCCTT\n+CCAGTTGAAACCACTTTCGCAGCTGGTCAATTTCTATTTCGCGCTGGCCGATGCTGTCCCAT\n+TGCATGAGCAGCTCGTAAAGCCTGATCGCGTGGGTGCTGTCCATCTTGGCCACGTCAGCCAA\n+GGCGTATTTGGTGAACTGTTTGGTGAGTTCCGTCAGGTACGGCAGCATGTCTTTGGTGAACC\n+TGAGTTCTACACGGCCCTCACCCTCCCGGTAGATGATTGTTTGCACCCAGCCGGTAATCATC\n+ACACTCGGTCTTTTCCCCTTGCCATTGGGCTCTTGGGT\n+>puc18_ORF.102 [1399-1459](-) type:complete length:60 frame:-3 start:CTG stop:TGA\n+CTGGTTGTAGGAAGATTCGATAGGGACACCCGCCATCGTCGCTATGTCCTCCGCCGTCAC\n+>puc18_ORF.103 [1264-1357](-) type:complete length:93 frame:-3 start:CTG stop:TGA\n+CTGGCTAATACAGGCCAGAACGATCCGCTGTTCCTGAACACTGAGGCGATACGCGGCCTCGA\n+CCAGGGCATTGCTTTTGTAAACCATTGGGGG\n+>puc18_ORF.104 [1120-1243](-) type:complete length:123 frame:-3 start:TTG stop:TAA\n+TTGTGTATAAGGGGACACTGTATCTGCGTCCCACAATACAACAAATCCGTCCCTTTACAACA\n+ACAAATCCGTCCCTTCTTAACAACAAATCCGTCCCTTAATGGCAACAAATCCGTCCCTTTT\n+>puc18_ORF.105 [694-991](-) type:complete length:297 frame:-3 start:CTG stop:TGA\n+CTGAAGGGGCGGGGGAGGCGTCTGGGCAATCCCCGTTTTACCAGTCCCCTATCGCCGCCTGA\n+GAGGGCGCAGGAAGCGAGTAATCAGGGTATCGAGGCGGATTCACCCTTGGCGTCCAACCAGC\n+GGCACCAGCGGCGCCTGAGAGGCCTACAGAGCGGTTGGACACCAAGGGGAGGGGCTAAGACC\n+GGTTTATCAGTCCCCTTTCCCTCGTTTCTTTCCAACGCGATAGCCCAGCAAGGCCGCCACCG\n+TTGCCACCGTCACCCCAGCAAGCACAGCCAGTGGCGTGTAATTGGGGTC\n+>puc18_ORF.106 [307-514](-) type:complete length:207 frame:-3 start:CTG stop:TAA\n+CTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGG\n+AGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGATCCACGCTCACCGGCTCCA\n+GATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTT\n+ATCCGCCTCCATCCAGTCTAT\n+>puc18_ORF.107 [148-235](-) type:complete length:87 frame:-3 start:CTG stop:TAG\n+CTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCT\n+CAGTACAATCTGCTCTGATGCCGCA\n'