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comparison vsnp_determine_ref_from_data.xml @ 1:b03e88e7bb1d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
author iuc
date Thu, 10 Dec 2020 15:25:22 +0000
parents 12f2b14549f6
children 6853676d2bae
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0:12f2b14549f6 1:b03e88e7bb1d
1 <tool id="vsnp_determine_ref_from_data" name="vSNP: determine reference" version="1.0.0"> 1 <tool id="vsnp_determine_ref_from_data" name="vSNP: determine reference" version="@WRAPPER_VERSION@.1" profile="@PROFILE@">
2 <description>from input data</description> 2 <description>from input data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
23 #else: 23 #else:
24 #set read2 = None 24 #set read2 = None
25 #end if 25 #end if
26 #else: 26 #else:
27 #set read1 = $input_type_cond.reads_collection['forward'] 27 #set read1 = $input_type_cond.reads_collection['forward']
28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) 28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
29 ln -s '${read1}' '${read1_identifier}' && 29 ln -s '${read1}' '${read1_identifier}' &&
30 #set read2 = $input_type_cond.reads_collection['reverse'] 30 #set read2 = $input_type_cond.reads_collection['reverse']
31 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 31 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
32 ln -s '${read2}' '${read2_identifier}' && 32 ln -s '${read2}' '${read2_identifier}' &&
33 #end if 33 #end if
34 34
35 python '$__tool_directory__/vsnp_determine_ref_from_data.py' 35 python '$__tool_directory__/vsnp_determine_ref_from_data.py'
36 --read1 '${read1_identifier}' 36 --read1 '${read1_identifier}'
65 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> 65 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
66 </when> 66 </when>
67 </conditional> 67 </conditional>
68 </inputs> 68 </inputs>
69 <outputs> 69 <outputs>
70 <data name="output_dbkey" format="txt" label="${tool.name} (dbkey) on ${on_string}"/> 70 <data name="output_dbkey" format="txt" label="${tool.name} on ${on_string} (dbkey)"/>
71 <data name="output_metrics" format="txt" label="${tool.name} (metrics) on ${on_string}"/> 71 <data name="output_metrics" format="txt" label="${tool.name} on ${on_string} (metrics)"/>
72 </outputs> 72 </outputs>
73 <tests> 73 <tests>
74 <!-- 1 single read --> 74 <!-- 1 single read -->
75 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2">
76 <param name="input_type" value="single"/> 76 <param name="input_type" value="single"/>
79 <output name="output_metrics" file="output_metrics.txt" ftype="txt"/> 79 <output name="output_metrics" file="output_metrics.txt" ftype="txt"/>
80 </test> 80 </test>
81 <!-- 1 set of paired reads --> 81 <!-- 1 set of paired reads -->
82 <test expect_num_outputs="2"> 82 <test expect_num_outputs="2">
83 <param name="input_type" value="pair"/> 83 <param name="input_type" value="pair"/>
84 <param name="read1" value="forward.fastq.gz" ftype="fastqsanger.gz"/> 84 <param name="read1" value="CMC_20E1_R1.fastq.gz" ftype="fastqsanger.gz"/>
85 <param name="read2" value="reverse.fastq.gz" ftype="fastqsanger.gz"/> 85 <param name="read2" value="CMC_20E1_R2.fastq.gz" ftype="fastqsanger.gz"/>
86 <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/> 86 <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/>
87 <output name="output_metrics" file="paired_metrics.txt" ftype="txt"/> 87 <output name="output_metrics" file="paired_metrics.txt" ftype="txt"/>
88 </test> 88 </test>
89 <!-- A collection of paired reads --> 89 <!-- A collection of paired reads -->
90 <test expect_num_outputs="2"> 90 <test expect_num_outputs="2">
91 <param name="input_type" value="paired"/> 91 <param name="input_type" value="paired"/>
92 <param name="reads_collection"> 92 <param name="reads_collection">
93 <collection type="paired"> 93 <collection type="paired">
94 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz"/> 94 <element name="forward" value="CMC_20E1_R1.fastq.gz" ftype="fastqsanger.gz"/>
95 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz"/> 95 <element name="reverse" value="CMC_20E1_R2.fastq.gz" ftype="fastqsanger.gz"/>
96 </collection> 96 </collection>
97 </param> 97 </param>
98 <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/> 98 <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/>
99 <output name="output_metrics" file="paired_metrics.txt" ftype="txt"/> 99 <output name="output_metrics" file="paired_collection_metrics.txt" ftype="txt"/>
100 </test> 100 </test>
101 </tests> 101 </tests>
102 <help> 102 <help>
103 **What it does** 103 **What it does**
104 104