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comparison sequence-splitter.xml @ 2:6dd4f53b9964 draft default tip

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"planemo upload for repository https://github.com/rplanel/galaxy-tools/tree/master/tools/sequence-splitter commit 98f957247a46eabf7e561bd94328b6a03a4d73b9"
author rplanel
date Sat, 21 Nov 2020 08:50:21 +0000
parents 7b509a1801e4
children
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1:7b509a1801e4 2:6dd4f53b9964
1 <tool id="sequence-splitter" name="Sequence Splitter" version="0.1.1"> 1 <tool id="sequence-splitter" name="Sequence Splitter" version="@WRAPPER_VERSION@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <requirements> 5 <expand macro="requirements" />
6 <requirement type="package" version="2.7.11">python</requirement>
7 <requirement type="package" version="1.73">biopython</requirement>
8 </requirements>
9 <edam_operations> 6 <edam_operations>
10 <edam_operation>operation_2409</edam_operation> 7 <edam_operation>operation_2409</edam_operation>
11 <edam_operation>operation_3359</edam_operation> 8 <edam_operation>operation_3359</edam_operation>
12 </edam_operations> 9 </edam_operations>
13 <edam_topics> 10 <edam_topics>
14 <edam_topic>topic_3307</edam_topic> 11 <edam_topic>topic_3307</edam_topic>
15 <edam_topic>topic_0080</edam_topic> 12 <edam_topic>topic_0080</edam_topic>
16 </edam_topics> 13 </edam_topics>
17 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code">
15 <![CDATA[
18 ln -s '$sequences' ./sequences.${sequences.ext} && 16 ln -s '$sequences' ./sequences.${sequences.ext} &&
19 python 17 python
20 '$__tool_directory__/sequence-splitter.py' 18 '$__tool_directory__/sequence-splitter.py'
21 -s ./sequences.$sequences.ext 19 -s ./sequences.$sequences.ext
22 #if $sequences.is_of_type("fasta") 20 #if $sequences.is_of_type("fasta")
28 -c $split_mode.chunk_size 26 -c $split_mode.chunk_size
29 #else 27 #else
30 -n $split_mode.nb_chunk 28 -n $split_mode.nb_chunk
31 #end if 29 #end if
32 -o 'outputs' 30 -o 'outputs'
33 ]]> </command> 31 ]]>
32 </command>
34 <inputs> 33 <inputs>
35 <param type="data" name="sequences" format="fasta,fastq"/> 34 <param type="data" name="sequences" format="fasta,fastq" />
36 <conditional name="split_mode"> 35 <conditional name="split_mode">
37 <param name="selector" type="select" label="Split by:"> 36 <param name="selector" type="select" label="Split by:">
38 <option value="chunk_size">Number of sequence(s) by chunk</option> 37 <option value="chunk_size">Number of sequence(s) by chunk</option>
39 <option value="nb_chunk">Number of chunk(s)</option> 38 <option value="nb_chunk">Number of chunk(s)</option>
40 </param> 39 </param>
41 <when value="chunk_size"> 40 <when value="chunk_size">
42 <param name="chunk_size" label="Chunk size" type="integer" min="1" value="100" help="How many sequences by chunk ?"/> 41 <param name="chunk_size" label="Chunk size" type="integer" min="1" value="100" help="How many sequences by chunk ?" />
43 </when> 42 </when>
44 <when value="nb_chunk"> 43 <when value="nb_chunk">
45 <param name="nb_chunk" label="Number of chunks" type="integer" min="1" value="10" help="How many chunks ?"/> 44 <param name="nb_chunk" label="Number of chunks" type="integer" min="1" value="10" help="How many chunks ?" />
46 </when> 45 </when>
47 </conditional> 46 </conditional>
48 </inputs> 47 </inputs>
49 <outputs> 48 <outputs>
50 <collection name="split_output" type="list" label="splitted sequences"> 49 <collection name="split_output" type="list" label="splitted sequences">
51 <discover_datasets pattern="(?P&lt;designation&gt;\w+-chunk-\d+)\.(?P&lt;ext&gt;.+)" directory="outputs" /> 50 <discover_datasets pattern="(?P&lt;designation&gt;\w+-chunk-\d+)\.(?P&lt;ext&gt;.+)" directory="outputs" />
52 </collection> 51 </collection>
53 <data format="text" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}"/> 52 <data format="txt" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}" />
54 </outputs> 53 </outputs>
55 <tests> 54 <tests>
56 <!-- CHUNK SIZE --> 55 <!-- CHUNK SIZE -->
57 <test> 56 <test>
58 <param name="sequences" value="sample.fastq"/> 57 <param name="sequences" value="sample.fastq" />
59 <conditional name="split_mode"> 58 <conditional name="split_mode">
60 <param name="selector" value="chunk_size"/> 59 <param name="selector" value="chunk_size" />
61 <param name="chunk_size" value="2"/> 60 <param name="chunk_size" value="2" />
62 </conditional> 61 </conditional>
63 <output_collection name="split_output" type="list" count="5"> 62 <output_collection name="split_output" type="list" count="5">
64 <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff"/> 63 <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff" />
65 <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff"/> 64 <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff" />
66 <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff"/> 65 <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff" />
67 <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff"/> 66 <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff" />
68 <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff"/> 67 <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff" />
69 </output_collection> 68 </output_collection>
70 </test> 69 </test>
71 <test> 70 <test>
72 <param name="sequences" value="sample.fasta"/> 71 <param name="sequences" value="sample.fasta" />
73 <conditional name="split_mode"> 72 <conditional name="split_mode">
74 <param name="selector" value="chunk_size" /> 73 <param name="selector" value="chunk_size" />
75 <param name="chunk_size" value="5"/> 74 <param name="chunk_size" value="5" />
76 </conditional> 75 </conditional>
77 <output_collection name="split_output" type="list" count="1"> 76 <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"/> 77 <element name="sequences-chunk-1" file="sample-5-chunk-1.fasta" ftype="fasta" compare="diff" />
79 </output_collection> 78 </output_collection>
80 </test> 79 </test>
81 <!-- NUMBER CHUNK --> 80 <!-- NUMBER CHUNK -->
82 <test> 81 <test>
83 <param name="sequences" value="sample.fastq"/> 82 <param name="sequences" value="sample.fastq" />
84 <conditional name="split_mode"> 83 <conditional name="split_mode">
85 <param name="selector" value="nb_chunk" /> 84 <param name="selector" value="nb_chunk" />
86 <param name="nb_chunk" value="2"/> 85 <param name="nb_chunk" value="2" />
87 </conditional> 86 </conditional>
88 <output_collection name="split_output" type="list" count="2"> 87 <output_collection name="split_output" type="list" count="2">
89 <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff"/> 88 <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff" />
90 <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff"/> 89 <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff" />
91 </output_collection> 90 </output_collection>
92 </test> 91 </test>
93 <test> 92 <test>
94 <param name="sequences" value="sample.fastq"/> 93 <param name="sequences" value="sample.fastq" />
95 <conditional name="split_mode"> 94 <conditional name="split_mode">
96 <param name="selector" value="nb_chunk" /> 95 <param name="selector" value="nb_chunk" />
97 <param name="nb_chunk" value="4"/> 96 <param name="nb_chunk" value="4" />
98 </conditional> 97 </conditional>
99 <output_collection name="split_output" type="list" count="4"> 98 <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"/> 99 <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"/> 100 <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"/> 101 <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"/> 102 <element name="sequences-chunk-4" file="sample-4-chunk-4.fastq" ftype="fastqsanger" compare="diff" />
104 </output_collection> 103 </output_collection>
105 </test> 104 </test>
106 <test> 105 <test>
107 <param name="sequences" value="sample.fasta"/> 106 <param name="sequences" value="sample.fasta" />
108 <conditional name="split_mode"> 107 <conditional name="split_mode">
109 <param name="selector" value="nb_chunk" /> 108 <param name="selector" value="nb_chunk" />
110 <param name="nb_chunk" value="10"/> 109 <param name="nb_chunk" value="10" />
111 </conditional> 110 </conditional>
112 <output_collection name="split_output" type="list" count="4"> 111 <output_collection name="split_output" type="list" count="4">
113 <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff"/> 112 <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff" />
114 <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff"/> 113 <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff" />
115 <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff"/> 114 <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff" />
116 <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff"/> 115 <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff" />
117 </output_collection> 116 </output_collection>
118 </test> 117 </test>
119 118
120 </tests> 119 </tests>
121 <help><![CDATA[ 120 <help>
121 <![CDATA[
122 Usage: 122 Usage:
123 123
124 sequence-splitter.py [-h] [-s SEQUENCES] [-f FORMAT] (-c CHUNK_SIZE | -n NB_CHUNK) [-o OUTPUT] 124 sequence-splitter.py [-h] [-s SEQUENCES] [-f FORMAT] (-c CHUNK_SIZE | -n NB_CHUNK) [-o OUTPUT]
125 125
126 Split fasta/fastq files 126 Split fasta/fastq files
142 142
143 -o OUTPUT, --output OUTPUT 143 -o OUTPUT, --output OUTPUT
144 The output directory where the chunks will be saved 144 The output directory where the chunks will be saved
145 145
146 146
147 ]]> </help> 147 ]]>
148 </help>
148 <expand macro="citations" /> 149 <expand macro="citations" />
149 </tool> 150 </tool>