Mercurial > repos > michal_klinka > trtools

comparison MergeSTR/mergeSTR.xml @ 1:8e8cf43f6836 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390
author michal_klinka
date Sun, 15 May 2022 15:23:59 +0000
parents ecf8c4f9f8ba
children
comparison
equal deleted inserted replaced
0:ecf8c4f9f8ba 1:8e8cf43f6836
101 <data name="stderr" label="STDERR output" format="txt"/> 101 <data name="stderr" label="STDERR output" format="txt"/>
102 </outputs> 102 </outputs>
103 103
104 104
105 <tests> 105 <tests>
106 <section name="main_params"> 106 <test>
107 <section name="required_arguments">
107 <param name="out" value="test_result"/> 108 <param name="out" value="test_result"/>
108 <param name="vcftype" value="hipstr"/> 109 <param name="vcftype" value="hipstr"/>
109 <repeat name="vcfs"> 110 <repeat name="vcfs">
110 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/> 111 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
111 </repeat> 112 </repeat>
112 <repeat name="vcfs"> 113 <repeat name="vcfs">
113 <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/> 114 <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/>
114 </repeat> 115 </repeat>
115 </section> 116 </section>
116 <section name="other"> 117 <section name="optional_arguments">
117 <param name="verbose" value="true"/> 118 <param name="verbose" value="true"/>
118 </section> 119 </section>
119 <output name="stdout" file="stdout.txt"> 120 <output name="stdout" file="stdout.txt">
120 <discovered_dataset designation="test_result"> 121 <discovered_dataset designation="test_result">
121 <!-- The vcf output itself can't be directly compared, because it contains the command that executed it, and that command is different for every run --> 122 <!-- The vcf output itself can't be directly compared, because it contains the command that executed it, and that command is different for every run -->
122 <assert_contents> 123 <assert_contents>
123 <has_size value="3106028" delta="100"/> 124 <has_size value="3106435" delta="100"/>
124 <has_text text="##fileformat=VCFv4.1"/> 125 <has_text text="##fileformat=VCFv4.1"/>
125 <has_n_lines n="9695"/> 126 <has_n_lines n="9658"/>
126 </assert_contents> 127 </assert_contents>
127 </discovered_dataset> 128 </discovered_dataset>
128 </output> 129 </output>
129 <output name="stderr" file="stderr.txt"/> 130 <output name="stderr" file="stderr.txt"/>
131 </test>
130 </tests> 132 </tests>
131 133
132 134
133 <help>usage: main.py [-h] --vcfs VCFS --out OUT [--vcftype VCFTYPE] 135 <help>sage: pygalgen [-h] --vcfs VCFS --out OUT [--vcftype VCFTYPE] [--update-sample-from-file] [--verbose] [--quiet]
134 [--update-sample-from-file] [--verbose] [--quiet] [--version] 136 [--version]
135 137
136 options: 138 options:
137 -h, --help show this help message and exit 139 -h, --help show this help message and exit
138 140
139 Required arguments: 141 Required arguments:
140 --vcfs VCFS Comma-separated list of VCF files to merge (must be sorted, 142 --vcfs VCFS Comma-separated list of VCF files to merge (must be sorted, bgzipped and indexed)
141 bgzipped and indexed) 143 --out OUT Prefix to name output files
142 --out OUT Prefix to name output files 144 --vcftype VCFTYPE ##!!## Name trh could not be loaded
143 --vcftype VCFTYPE ##!!## Name trh could not be loaded
144 145
145 Special merge options: 146 Special merge options:
146 --update-sample-from-file 147 --update-sample-from-file
147 Use file names, rather than sample header names, when merging 148 Use file names, rather than sample header names, when merging
148 149
149 Optional arguments: 150 Optional arguments:
150 --verbose Print out extra info 151 --verbose Print out extra info
151 --quiet Don't print out anything 152 --quiet Don't print out anything
152 153
153 Version: 154 Version:
154 --version show program's version number and exit 155 --version show program's version number and exit
155 </help> 156 </help>
156 157
157 158
158 <citations> 159 <citations>
159 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide 160 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide