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comparison megahit_wrapper.xml @ 3:98242353faa4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit aaac63680661511b90969309434043ce946d6501
author iuc
date Mon, 14 May 2018 06:11:34 -0400
parents edc663aadfa8
children de387b2b2803
comparison
equal deleted inserted replaced
2:edc663aadfa8 3:98242353faa4
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="megahit" name="MEGAHIT" version="@VERSION@.2"> 2 <tool id="megahit" name="MEGAHIT" version="@VERSION@.3">
3 <description>for metagenomics assembly</description> 3 <description>for metagenomics assembly</description>
4 <macros> 4 <macros>
5 <token name="@VERSION@">1.1.2</token> 5 <token name="@VERSION@">1.1.2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
12 megahit 12 megahit
13 #if $input_option.choice == 'paired' 13 #if $input_option.choice == 'paired'
14 -1 '${input_option.fastq_input1}' 14 -1 '${input_option.fastq_input1}'
15 -2 '${input_option.fastq_input2}' 15 -2 '${input_option.fastq_input2}'
16 #else if $input_option.choice == 'paired_collection' 16 #else if $input_option.choice == 'paired_collection'
17 -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) } 17
18 -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) } 18 #if $input_option.batchmode.processmode == 'merge':
19 -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.batchmode.pair_input_list]) }
20 -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.batchmode.pair_input_list]) }
21 #else:
22 -1 '${input_option.batchmode.pair_input.forward}'
23 -2 '${input_option.batchmode.pair_input.reverse}'
24 #end if
19 #else 25 #else
20 -r '${input_option.single_files}' 26 -r '${input_option.single_files}'
21 #end if 27 #end if
22 ##basic assembly 28 ##basic assembly
23 --min-count '${basic_section.min_count}' 29 --min-count '${basic_section.min_count}'
49 <when value="paired"> 55 <when value="paired">
50 <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/> 56 <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>
51 <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/> 57 <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/>
52 </when> 58 </when>
53 <when value="paired_collection"> 59 <when value="paired_collection">
54 <param name="fastq_input1" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="list:paired" label="Select a paired collection"/> 60 <conditional name="batchmode">
61 <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one assembly dataset for each fastq pair-end dataset. Selecting the merge option will produce one assembly dataset for all input fastq pair-end datasets" display="radio">
62 <option value="individual" selected="true">Run individually</option>
63 <option value="merge">Merge all fastq pair-end</option>
64 </param>
65 <when value="individual">
66 <param name="pair_input" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="paired" label="Select a paired collection"/>
67 </when>
68 <when value="merge">
69 <param name="pair_input_list" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="list:paired" label="Select a paired collection"/>
70 </when>
71 </conditional>
55 </when> 72 </when>
56 </conditional> 73 </conditional>
57 <section name="basic_section" title="Basic assembly options" expanded="True"> 74 <section name="basic_section" title="Basic assembly options" expanded="True">
58 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" /> 75 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
59 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/> 76 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
79 <test> 96 <test>
80 <conditional name="input_option"> 97 <conditional name="input_option">
81 <param name="choice" value="single"/> 98 <param name="choice" value="single"/>
82 <param name="single_files" value="refExample.fa" ftype="fasta"/> 99 <param name="single_files" value="refExample.fa" ftype="fasta"/>
83 </conditional> 100 </conditional>
84 <output name="output" file="single_result.fa"/> 101 <output name="output">
102 <assert_contents>
103 <has_line_matching expression=">k21_1 flag=3 multi=1.0486 len=576" />
104 </assert_contents>
105 </output>
85 </test> 106 </test>
86 <test> 107 <test>
87 <conditional name="input_option"> 108 <conditional name="input_option">
88 <param name="choice" value="paired"/> 109 <param name="choice" value="paired"/>
89 <param name="fastq_input1" value="paired-fq1.fa"/> 110 <param name="fastq_input1" value="paired-fq1.fa"/>
90 <param name="fastq_input2" value="paired-fq2.fa"/> 111 <param name="fastq_input2" value="paired-fq2.fa"/>
91 </conditional> 112 </conditional>
92 <output name="output" file="paired_result.fa"/> 113 <output name="output" file="paired_result.fa"/>
93 </test> 114 </test>
94 <test> 115 <test>
95 <conditional name="input_option"> 116 <conditional name="input_option">
96 <param name="choice" value="paired_collection"/> 117 <param name="choice" value="paired_collection"/>
97 <param name="fastq_input1"> 118 <conditional name="batchmode">
98 <collection type="list:paired"> 119 <param name="processmode" value="merge"/>
99 <element name="Pair1"> 120 <param name="pair_input_list">
100 <collection type="paired"> 121 <collection type="list:paired">
101 <element name="forward" value="paired-fq1.fa" ftype="fasta"/> 122 <element name="Pair1">
102 <element name="reverse" value="paired-fq2.fa" ftype="fasta"/> 123 <collection type="paired">
103 </collection> 124 <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
104 </element> 125 <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
105 </collection> 126 </collection>
106 </param> 127 </element>
128 </collection>
129 </param>
107 </conditional> 130 </conditional>
108 <output name="output" file="paired_result.fa"/> 131 </conditional>
132 <output name="output" file="paired_result.fa"/>
109 </test> 133 </test>
110 </tests> 134 </tests>
111 <help><![CDATA[ 135 <help><![CDATA[
112 136
113 **What it does** 137 **What it does**