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comparison orfipy.xml @ 1:6926cec0bc13 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
author iuc
date Thu, 22 Sep 2022 14:03:07 +0000
parents 4dd6001987b5
children
comparison
equal deleted inserted replaced
0:4dd6001987b5 1:6926cec0bc13
1 <tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy0" profile="21.05"> 1 <tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>a versatile ORF finder</description> 2 <description>a versatile ORF finder</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
25 #end if 25 #end if
26 #end for 26 #end for
27 --strand $strand 27 --strand $strand
28 #if $min: 28 #if $min:
29 --min $min 29 --min $min
30 #end if
31 #if $max:
32 --max $max
30 #end if 33 #end if
31 --table $table 34 --table $table
32 #if $start: 35 #if $start:
33 --start '$start' 36 --start '$start'
34 #end if 37 #end if
82 <option value="f">Forward</option> 85 <option value="f">Forward</option>
83 <option value="r">Reverse</option> 86 <option value="r">Reverse</option>
84 </param> 87 </param>
85 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs" 88 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
86 help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/> 89 help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
90 <param argument="--max" type="integer" min="0" optional="true" label="Maximum length of ORFs"
91 help="This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000."/>
87 <param argument="--start" type="text" optional="true" label="Start codon(s) to use" 92 <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
88 help="A comma-separated list without spaces. Only ATCG and comma are allowed"> 93 help="A comma-separated list without spaces. Only ATCG and comma are allowed">
89 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator> 94 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
90 </param> 95 </param>
91 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use" 96 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"
137 <param name="input1" value="orfipy.fa.gz"/> 142 <param name="input1" value="orfipy.fa.gz"/>
138 <param name="out_files" value="DNA"/> 143 <param name="out_files" value="DNA"/>
139 <param name="min" value="100"/> 144 <param name="min" value="100"/>
140 <param name="partial_5" value="true"/> 145 <param name="partial_5" value="true"/>
141 <output name="out_dna" file="test2.fa"/> 146 <output name="out_dna" file="test2.fa"/>
147 </test>
148 <test expect_num_outputs="1">
149 <param name="input1" value="orfipy.fa.gz"/>
150 <param name="out_files" value="DNA"/>
151 <param name="max" value="100000000"/>
152 <output name="out_dna" file="test3.fa"/>
142 </test> 153 </test>
143 </tests> 154 </tests>
144 <help><![CDATA[ 155 <help><![CDATA[
145 **What it does** 156 **What it does**
146 157