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comparison obiconvert.xml @ 3:374fd9feb032 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:36:34 +0000
parents 6259965de501
children e328ced6cf0a
comparison
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2:4d705e3443a7 3:374fd9feb032
1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@"> 1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>converts sequence files to different output formats</description> 2 <description>converts sequence files to different output formats</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 8 <command><![CDATA[
9 <command> 9 @GUNZIP_INPUT@
10 <![CDATA[ 10
11 obiconvert 11 obiconvert
12 #if $db 12 #if $db
13 -d '$db' 13 -d '$db'
14 #end if 14 #end if
15 #if $tax 15 #if $tax
16 -t '$tax' 16 -t '$tax'
17 #end if 17 #end if
18 ${options_inputtype} 18 @INPUT_FORMAT@
19 ${options_seqtype} 19 @OUT_FORMAT@
20 --${out_format}-output
21 ${uppercase} 20 ${uppercase}
22 ${ecopcrdb} 21 ${ecopcrdb}
23 #if str( $ecopcrdb) == "--ecopcrdb" 22 #if str( $ecopcrdb) == "--ecopcrdb"
24 --ecopcrdb-output=${ecopcrdb_output} 23 --ecopcrdb-output=${ecopcrdb_output}
25 #end if 24 #end if
26 '${input}' > '${output}' 25 input
27 ]]> 26 @GZIP_OUTPUT@
28 27 > '${output}'
29 </command> 28 @GENERATE_GALAXY_JSON@
30 29 ]]></command>
31 <inputs> 30 <inputs>
32 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" /> 31 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" />
33 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" /> 32 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
34 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/> 33 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
35 <param name="options_inputtype" type="select" label="Specify the input datatype"> 34 <expand macro="input_format_options_macro"/>
36 <expand macro="inputtype"/> 35 <expand macro="out_format_macro"/>
37 </param>
38 <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
39 <option value="--nuc" selected="true">nucleic</option>
40 <option value="--prot">protein</option>
41 </param>
42 <param name="out_format" type="select" label="Output data type">
43 <option value="fasta" selected="true">fasta</option>
44 <option value="fastq">fastq</option>
45 </param>
46 <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file" /> 36 <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file" />
47 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" /> 37 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" />
48
49 </inputs> 38 </inputs>
50 <outputs> 39 <outputs>
51 <data format="txt" name="ecopcrdb_output" label="result.ecopcrdb with ${tool.name} on ${on_string}"> 40 <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
52 <filter>ecopcrdb == True</filter> 41 <filter>ecopcrdb == True</filter>
53 </data> 42 </data>
54 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" > 43 <data format="auto" name="output"/>
55 <change_format>
56 <when input="out_format" value="fastq" format="fastq" />
57 </change_format>
58 </data>
59 </outputs> 44 </outputs>
60 <tests> 45 <tests>
61 <test> 46 <test>
62 <param name="input" value="output_obisort.fasta" /> 47 <param name="input" value="output_obisort.fasta" />
63 <param name="options_inputtype" value="fasta"/> 48 <param name="options_inputtype" value="--fasta"/>
64 <param name="options_seqtype" value="--nuc"/> 49 <param name="options_seqtype" value="--nuc"/>
65 <param name="out_format" value="fasta"/> 50 <param name="out_format" value="fasta"/>
66 <param name="ecopcrdb" value="False"/> 51 <param name="ecopcrdb" value="false"/>
67 <param name="uppercase" value="True"/> 52 <param name="uppercase" value="true"/>
68 <output name="output" file="output_obiconvert.fasta" ftype="fasta"/> 53 <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
69 </test> 54 </test>
70 </tests> 55 </tests>
71 <help><![CDATA[ 56 <help><![CDATA[
72 57