Mercurial > repos > iuc > vsnp_determine_ref_from_data
comparison vsnp_determine_ref_from_data.xml @ 1:b03e88e7bb1d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
author | iuc |
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date | Thu, 10 Dec 2020 15:25:22 +0000 |
parents | 12f2b14549f6 |
children | 6853676d2bae |
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0:12f2b14549f6 | 1:b03e88e7bb1d |
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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 |