Mercurial > repos > brinkmanlab > biopython_convert

comparison biopython-convert.xml @ 5:1c71c770bfd4 draft default tip

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planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit cae3bd2f937dee563791707ffb4aab8fe5b7e13b
author brinkmanlab
date Wed, 27 Jul 2022 19:49:20 +0000
parents d9ae46bb9f09
children
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4:a5cb5e374399 5:1c71c770bfd4
1 <tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.0" profile="16.04"> 1 <tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.1" profile="16.04">
2 <description>Interconvert between the various sequence file formats that BioPython supports</description> 2 <description>Interconvert between the various sequence file formats that BioPython supports</description>
3 <edam_topics> 3 <edam_topics>
4 <edam_topic>topic_0091</edam_topic> 4 <edam_topic>topic_0091</edam_topic>
5 </edam_topics> 5 </edam_topics>
6 <edam_operations> 6 <edam_operations>
9 <edam_operation>operation_3359</edam_operation> 9 <edam_operation>operation_3359</edam_operation>
10 <edam_operation>operation_0224</edam_operation> 10 <edam_operation>operation_0224</edam_operation>
11 <edam_operation>operation_3695</edam_operation> 11 <edam_operation>operation_3695</edam_operation>
12 </edam_operations> 12 </edam_operations>
13 <requirements> 13 <requirements>
14 <requirement type="package" version="1.0.4">biopython.convert</requirement> 14 <requirement type="package" version="1.3.3">biopython.convert</requirement>
15 </requirements> 15 </requirements>
16 <version_command><![CDATA[ biopython.convert -v ]]></version_command> 16 <version_command><![CDATA[ biopython.convert -v ]]></version_command>
17 <command detect_errors="aggressive"><![CDATA[ 17 <command detect_errors="aggressive"><![CDATA[
18 #if $bioperl 18 #if $bioperl
19 #set $script = 'python ' + $__tool_directory__ + '/bioperl_compat.py' 19 #set $script = 'python ' + $__tool_directory__ + '/bioperl_compat.py'
60 <option value="sff">sff</option> 60 <option value="sff">sff</option>
61 <option value="stockholm">stockholm</option> 61 <option value="stockholm">stockholm</option>
62 <option value="tab">tab</option> 62 <option value="tab">tab</option>
63 <option value="qual">qual</option> 63 <option value="qual">qual</option>
64 <option value="gff3">gff3</option> 64 <option value="gff3">gff3</option>
65 <option value="yaml">yaml</option>
66 <option value="json">json</option>
67 <option value="text">text</option>
65 </param> 68 </param>
66 <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" /> 69 <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" />
67 <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" /> 70 <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" />
68 <param name="query" type="text" label="Query records, keeping only what matches path" help="Provide a JMESPath selecting records to keep. The root is the list of records. The path must return a list of records."> 71 <param name="query" type="text" label="Query records, keeping only what matches path" help="Provide a JMESPath selecting records to keep. The root is the list of records. The path must return a list of records.">
69 <sanitizer> 72 <sanitizer>
100 <when input="output_type" value="sff" format="sff" /> 103 <when input="output_type" value="sff" format="sff" />
101 <when input="output_type" value="stockholm" format="stockholm" /> 104 <when input="output_type" value="stockholm" format="stockholm" />
102 <when input="output_type" value="tab" format="tabular" /> 105 <when input="output_type" value="tab" format="tabular" />
103 <when input="output_type" value="qual" format="qual" /> 106 <when input="output_type" value="qual" format="qual" />
104 <when input="output_type" value="gff3" format="gff3" /> 107 <when input="output_type" value="gff3" format="gff3" />
108 <when input="output_type" value="yaml" format="yaml" />
109 <when input="output_type" value="json" format="json" />
110 <when input="output_type" value="text" format="txt" />
105 </change_format> 111 </change_format>
106 </data> 112 </data>
107 <collection name="split_output" type="list" label="Output split per record from ${tool.name} on ${on_string}"> 113 <collection name="split_output" type="list" label="Output split per record from ${tool.name} on ${on_string}">
108 <filter>split</filter> 114 <filter>split</filter>
109 <discover_datasets pattern=".*" directory="output" format="$output_type" /> 115 <discover_datasets pattern=".*" directory="output" format="$output_type" />