Mercurial > repos > artbio > lumpy_smoove

comparison lumpy_smoove.xml @ 6:ad8853ee9909 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
author artbio
date Sun, 14 Feb 2021 23:59:42 +0000
parents bd4135caa3fa
children 8b0005fdfd04
comparison
equal deleted inserted replaced
5:bd4135caa3fa 6:ad8853ee9909
1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy5"> 1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy6">
2 <description>find structural variants using the smoove workflow</description> 2 <description>find structural variants using the smoove workflow</description>
3 <macros> 3 <macros>
4 <import>macro_lumpy_smoove.xml</import> 4 <import>macro_lumpy_smoove.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
100 <param name="reference_source_selector" value="history" /> 100 <param name="reference_source_selector" value="history" />
101 <param name="ref_file" value="chrI-ce11.fa"/> 101 <param name="ref_file" value="chrI-ce11.fa"/>
102 <param name="choices" value="yes"/> 102 <param name="choices" value="yes"/>
103 <param name="bedmask" value="exclude.bed"/> 103 <param name="bedmask" value="exclude.bed"/>
104 <param name="prpos" value="no"/> 104 <param name="prpos" value="no"/>
105 <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="8"/> 105 <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="12"/>
106 </test> 106 </test>
107 <test> 107 <test>
108 <param name="reference_source_selector" value="history" /> 108 <param name="reference_source_selector" value="history" />
109 <param name="ref_file" value="chrI-ce11.fa"/> 109 <param name="ref_file" value="chrI-ce11.fa"/>
110 <param name="normal_bam" value="celegans_RG_1.bam"/> 110 <param name="normal_bam" value="celegans_RG_1.bam"/>
111 <param name="tumor_bam" value="celegans_RG_2.bam"/> 111 <param name="tumor_bam" value="celegans_RG_2.bam"/>
112 <param name="choices" value="yes"/> 112 <param name="choices" value="yes"/>
113 <param name="bedmask" value="exclude.bed"/> 113 <param name="bedmask" value="exclude.bed"/>
114 <param name="prpos" value="no"/> 114 <param name="prpos" value="no"/>
115 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/> 115 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="12"/>
116 </test> 116 </test>
117 <test> 117 <test>
118 <param name="reference_source_selector" value="history" /> 118 <param name="reference_source_selector" value="history" />
119 <param name="ref_file" value="chrI-ce11.fa"/> 119 <param name="ref_file" value="chrI-ce11.fa"/>
120 <param name="normal_bam" value="celegans_RG_1.bam"/> 120 <param name="normal_bam" value="celegans_RG_1.bam"/>
121 <param name="tumor_bam" value="celegans_RG_2.bam"/> 121 <param name="tumor_bam" value="celegans_RG_2.bam"/>
122 <param name="choices" value="no"/> 122 <param name="choices" value="no"/>
123 <param name="prpos" value="no"/> 123 <param name="prpos" value="no"/>
124 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/> 124 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="12"/>
125 </test> 125 </test>
126 <test> 126 <test>
127 <param name="reference_source_selector" value="history" /> 127 <param name="reference_source_selector" value="history" />
128 <param name="ref_file" value="chrI-ce11.fa"/> 128 <param name="ref_file" value="chrI-ce11.fa"/>
129 <param name="normal_bam" value="celegans_RG_2.bam"/> 129 <param name="normal_bam" value="celegans_RG_2.bam"/>
130 <param name="tumor_bam" value="celegans_RG_1.bam"/> 130 <param name="tumor_bam" value="celegans_RG_1.bam"/>
131 <param name="choices" value="no"/> 131 <param name="choices" value="no"/>
132 <param name="prpos" value="no"/> 132 <param name="prpos" value="no"/>
133 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/> 133 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="12"/>
134 </test> 134 </test>
135 <test> 135 <test>
136 <param name="reference_source_selector" value="history" /> 136 <param name="reference_source_selector" value="history" />
137 <param name="ref_file" value="chrI-ce11.fa"/> 137 <param name="ref_file" value="chrI-ce11.fa"/>
138 <param name="normal_bam" value="celegans_RG_1.bam"/> 138 <param name="normal_bam" value="celegans_RG_1.bam"/>
139 <param name="tumor_bam" value="celegans_RG_2.bam"/> 139 <param name="tumor_bam" value="celegans_RG_2.bam"/>
140 <param name="choices" value="no"/> 140 <param name="choices" value="no"/>
141 <param name="prpos" value="yes"/> 141 <param name="prpos" value="yes"/>
142 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/> 142 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="12"/>
143 </test> 143 </test>
144 <test> 144 <test>
145 <param name="reference_source_selector" value="history" /> 145 <param name="reference_source_selector" value="history" />
146 <param name="plan_choice" value="single" /> 146 <param name="plan_choice" value="single" />
147 <param name="ref_file" value="chrI-ce11.fa"/> 147 <param name="ref_file" value="chrI-ce11.fa"/>
148 <param name="single_bam" value="celegans_RG_1.bam"/> 148 <param name="single_bam" value="celegans_RG_1.bam"/>
149 <param name="choices" value="no"/> 149 <param name="choices" value="no"/>
150 <param name="prpos" value="no"/> 150 <param name="prpos" value="no"/>
151 <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/> 151 <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="12"/>
152 </test> 152 </test>
153 </tests> 153 </tests>
154 154
155 <help> 155 <help>
156 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves 156 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves