Mercurial > repos > rplanel > sequence_splitter

comparison sequence-splitter.xml @ 1:7b509a1801e4 draft

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"planemo upload for repository https://github.com/rplanel/galaxy-tools/tree/master/tools/sequence-splitter commit 85ffc2e3805940c0ebb21d5450b86524bd788d7b"
author rplanel
date Tue, 20 Aug 2019 09:46:49 -0400
parents 3e33310a7082
children 6dd4f53b9964
comparison
equal deleted inserted replaced
0:3e33310a7082 1:7b509a1801e4
1 <tool id="sequence-splitter" name="Sequence Splitter" version="0.1.0"> 1 <tool id="sequence-splitter" name="Sequence Splitter" version="0.1.1">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
2 <requirements> 5 <requirements>
3 <requirement type="package" version="2.7.11">python</requirement> 6 <requirement type="package" version="2.7.11">python</requirement>
4 <requirement type="package" version="1.73">biopython</requirement> 7 <requirement type="package" version="1.73">biopython</requirement>
5 </requirements> 8 </requirements>
6 <edam_operations> 9 <edam_operations>
48 <discover_datasets pattern="(?P&lt;designation&gt;\w+-chunk-\d+)\.(?P&lt;ext&gt;.+)" directory="outputs" /> 51 <discover_datasets pattern="(?P&lt;designation&gt;\w+-chunk-\d+)\.(?P&lt;ext&gt;.+)" directory="outputs" />
49 </collection> 52 </collection>
50 <data format="text" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}"/> 53 <data format="text" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}"/>
51 </outputs> 54 </outputs>
52 <tests> 55 <tests>
53 <test> 56 <!-- CHUNK SIZE -->
54 <param name="sequences" value="sample.fasta"/>
55 <conditional name="split_mode">
56 <param name="selector" value="chunk_size"/>
57 <param name="chunk_size" value="2"/>
58 </conditional>
59 <output_collection name="split_output" type="list" count="2">
60 <element name="sequences-chunk-1" file="sample-chunk-1.fasta" ftype="fasta"/>
61 <element name="sequences-chunk-2" file="sample-chunk-2.fasta" ftype="fasta"/>
62 </output_collection>
63 </test>
64 <test> 57 <test>
65 <param name="sequences" value="sample.fastq"/> 58 <param name="sequences" value="sample.fastq"/>
66 <conditional name="split_mode"> 59 <conditional name="split_mode">
67 <param name="selector" value="chunk_size"/> 60 <param name="selector" value="chunk_size"/>
68 <param name="chunk_size" value="2"/> 61 <param name="chunk_size" value="2"/>
69 </conditional> 62 </conditional>
70 <output_collection name="split_output" type="list" count="5"> 63 <output_collection name="split_output" type="list" count="5">
71 <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger"/> 64 <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
72 <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger"/> 65 <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
73 <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger"/> 66 <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff"/>
74 <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger"/> 67 <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff"/>
75 <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger"/> 68 <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff"/>
76 </output_collection> 69 </output_collection>
77 </test> 70 </test>
78 71 <test>
72 <param name="sequences" value="sample.fasta"/>
73 <conditional name="split_mode">
74 <param name="selector" value="chunk_size" />
75 <param name="chunk_size" value="5"/>
76 </conditional>
77 <output_collection name="split_output" type="list" count="1">
78 <element name="sequences-chunk-1" file="sample-5-chunk-1.fasta" ftype="fasta" compare="diff"/>
79 </output_collection>
80 </test>
81 <!-- NUMBER CHUNK -->
79 <test> 82 <test>
80 <param name="sequences" value="sample.fastq"/> 83 <param name="sequences" value="sample.fastq"/>
81 <conditional name="split_mode"> 84 <conditional name="split_mode">
82 <param name="selector" value="nb_chunk" /> 85 <param name="selector" value="nb_chunk" />
83 <param name="nb_chunk" value="2"/> 86 <param name="nb_chunk" value="2"/>
84 </conditional> 87 </conditional>
85 <output_collection name="split_output" type="list" count="2"> 88 <output_collection name="split_output" type="list" count="2">
86 <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger"/> 89 <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
87 <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger"/> 90 <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
91 </output_collection>
92 </test>
93 <test>
94 <param name="sequences" value="sample.fastq"/>
95 <conditional name="split_mode">
96 <param name="selector" value="nb_chunk" />
97 <param name="nb_chunk" value="4"/>
98 </conditional>
99 <output_collection name="split_output" type="list" count="4">
100 <element name="sequences-chunk-1" file="sample-4-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
101 <element name="sequences-chunk-2" file="sample-4-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
102 <element name="sequences-chunk-3" file="sample-4-chunk-3.fastq" ftype="fastqsanger" compare="diff"/>
103 <element name="sequences-chunk-4" file="sample-4-chunk-4.fastq" ftype="fastqsanger" compare="diff"/>
88 </output_collection> 104 </output_collection>
89 </test> 105 </test>
90 <test> 106 <test>
91 <param name="sequences" value="sample.fasta"/> 107 <param name="sequences" value="sample.fasta"/>
92 <conditional name="split_mode"> 108 <conditional name="split_mode">
93 <param name="selector" value="nb_chunk" /> 109 <param name="selector" value="nb_chunk" />
94 <param name="nb_chunk" value="10"/> 110 <param name="nb_chunk" value="10"/>
95 </conditional> 111 </conditional>
96 <output_collection name="split_output" type="list" count="4"> 112 <output_collection name="split_output" type="list" count="4">
97 <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta"/> 113 <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff"/>
98 <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta"/> 114 <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff"/>
99 <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta"/> 115 <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff"/>
100 <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta"/> 116 <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff"/>
101 </output_collection> 117 </output_collection>
102 </test> 118 </test>
103 119
104 </tests> 120 </tests>
105 <help><![CDATA[ 121 <help><![CDATA[
127 -o OUTPUT, --output OUTPUT 143 -o OUTPUT, --output OUTPUT
128 The output directory where the chunks will be saved 144 The output directory where the chunks will be saved
129 145
130 146
131 ]]> </help> 147 ]]> </help>
148 <expand macro="citations" />
132 </tool> 149 </tool>