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comparison splitFasta.xml @ 1:87bdbac78136 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 31945d5d8c5ebee64ebf29c6ea022fb831f47274"
author rnateam
date Mon, 21 Sep 2020 15:41:01 +0000
parents f6d6b62540f8
children
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0:f6d6b62540f8 1:87bdbac78136
1 <tool id="rbc_splitfasta" name="Split Fasta" version="0.2.0"> 1 <tool id="rbc_splitfasta" name="Split Fasta" version="0.4.0">
2 <description>files into a collection</description> 2 <description>files into a collection</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.65">biopython</requirement> 4 <requirement type="package" version="1.76">biopython</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="aggressive">
7 <exit_code range="1:" />
8 </stdio>
9 <command interpreter="python">
10 <![CDATA[ 7 <![CDATA[
11 splitFasta.py $inputFile 8 #if $splitmode.splitmode_select == "each":
9 python $__tool_directory__/split_fasta.py '$inputFile'
10 #else if $splitmode.splitmode_select == "chunks":
11 python $__tool_directory__/split_fasta.py '$inputFile' $splitmode.num_chunks
12 #end if
12 ]]></command> 13 ]]></command>
13 <inputs> 14 <inputs>
14 <param name="inputFile" type="data" format="fasta" label="Fasta file to split"/> 15 <param name="inputFile" type="data" format="fasta" label="Fasta file to split"/>
16 <conditional name="splitmode">
17 <param name="splitmode_select" type="select" label="Split mode">
18 <option value="each">Each sequence in its own dataset</option>
19 <option value="chunks">Split into a number of chunks</option>
20 </param>
21 <when value="chunks">
22 <param name="num_chunks" type="integer" value="10" label="Number of chunks to split into" />
23 </when>
24 <when value="each"/>
25 </conditional>
15 </inputs> 26 </inputs>
16 <outputs> 27 <outputs>
17 <collection name="splitted_fasta" type="list" label="Sequence collection in FASTA format"> 28 <collection name="splitted_fasta" type="list" label="${tool.name} on ${on_string}">
18 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="splits" ext="fasta" visible="false"/> 29 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="splits" ext="fasta" visible="false"/>
19 </collection> 30 </collection>
20 </outputs> 31 </outputs>
21 <tests> 32 <tests>
22 <test> 33 <test>
23 <param name="inputFile" value="test.fasta" /> 34 <param name="inputFile" value="sample1.fasta" />
24 <output_collection name="splitted_fasta"> 35 <param name="splitmode|splitmode_select" value="each" />
25 <element name="ID1.fasta" file="ID1_result1.fasta" ftype="fasta" /> 36 <output_collection name="splitted_fasta" count="3">
26 <element name="ID2.fasta" file="ID2_result1.fasta" ftype="fasta" /> 37 <element name="ID1" file="ID1.fasta" ftype="fasta" />
27 <element name="ID3.fasta" file="ID3_result1.fasta" ftype="fasta" /> 38 <element name="ID2" file="ID2.fasta" ftype="fasta" />
39 <element name="ID3" file="ID3.fasta" ftype="fasta" />
40 </output_collection>
41 </test>
42 <test>
43 <param name="inputFile" value="sample2.fasta" />
44 <param name="splitmode|splitmode_select" value="chunks" />
45 <param name="num_chunks" value="4" />
46 <output_collection name="splitted_fasta" count="4">
47 <element name="part1" file="part1.fasta" ftype="fasta" />
48 <element name="part2" file="part2.fasta" ftype="fasta" />
49 <element name="part3" file="part3.fasta" ftype="fasta" />
50 <element name="part4" file="part4.fasta" ftype="fasta" />
28 </output_collection> 51 </output_collection>
29 </test> 52 </test>
30 </tests> 53 </tests>
31 <help><![CDATA[ 54 <help><![CDATA[
32 Takes an input file and writes each consecutive two lines to a separate file, in a dataset collection. 55 Takes an input FASTA file and writes entries (i.e. sequences) to separate datasets, which are organized in a dataset collection.
56 There are two modes: 1) each sequence is written to its own data set which is named by the ID of the sequence or 2) The file is split into a given number of chunks which are numbered.
33 ]]></help> 57 ]]></help>
34 <citations> 58 <citations>
35 <citation type="bibtex"> 59 <citation type="bibtex">
36 @ARTICLE{bgruening_galaxytools, 60 @ARTICLE{bgruening_galaxytools,
37 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche}, 61 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},