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comparison lumpy.xml @ 1:a006d42dd759 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
author drosofff
date Tue, 06 Dec 2016 09:29:31 -0500
parents 8b3daa745d9b
children b1e152172de9
comparison
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0:8b3daa745d9b 1:a006d42dd759
69 </conditional> 69 </conditional>
70 70
71 </inputs> 71 </inputs>
72 72
73 <outputs> 73 <outputs>
74 <data format="tabular" name="histogram" type="data" label="${input_file.element_identifier} Fragment size distribution"> 74 <data format="tabular" name="histogram" type="data" label="Lumpy on ${input_file.element_identifier}: Fragment size distribution">
75 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 75 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
76 </data> 76 </data>
77 <data format="bam" name="splits" type="data" label="${input_file.element_identifier} Split Reads (Bam format)"/> 77 <data format="bam" name="splits" type="data" label="Lumpy on ${input_file.element_identifier}: Split Reads (Bam format)"/>
78 <data format="bam" name="discordants" type="data" label="${input_file.element_identifier} Discordant Pairs (Bam format)"> 78 <data format="bam" name="discordants" type="data" label="Lumpy on ${input_file.element_identifier}: Discordant Pairs (Bam format)">
79 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 79 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
80 </data> 80 </data>
81 <data format="vcf" name="vcf_call" type="data" label="${input_file.element_identifier} Variant Calling (vcf format)"/> 81 <data format="vcf" name="vcf_call" type="data" label="Lumpy on ${input_file.element_identifier}: Variant Calling (vcf format)"/>
82 </outputs> 82 </outputs>
83 83
84 <tests> 84 <tests>
85 <test> 85 <test>
86 <param name="input_file" value="sr.input.bam" ftype="bam"/> 86 <param name="input_file" value="sr.input.bam" ftype="bam"/>
91 <output name="vcf_call" file="output.vcf" ftype="vcf"/> 91 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
92 </test> 92 </test>
93 </tests> 93 </tests>
94 94
95 <help> 95 <help>
96 Some help required 96
97 **lumpy-sv manual**
98
99 Read the lumpy-sv_ documentation for details on using lumpy.
100
101 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv
102
103 **lumpy options**
104
105 v 0.2.13
106 Author: Ryan Layer (rl6sf@virginia.edu)
107
108 Summary: Find structural variations in various signals.
109
110 Options::
111
112 -g Genome file (defines chromosome order)
113 -e Show evidence for each call
114 -w File read windows size (default 1000000)
115 -mw minimum weight for a call
116 -msw minimum per-sample weight for a call
117 -tt trim threshold
118 -x exclude file bed file
119 -t temp file prefix, must be to a writeable directory
120 -P output probability curve for each variant
121 -b output BEDPE instead of VCF
122 -sr bam_file:&lt;file name&gt;,
123 id:&lt;sample name&gt;,
124 back_distance:&lt;distance&gt;,
125 min_mapping_threshold:&lt;mapping quality&gt;,
126 weight:&lt;sample weight&gt;,
127 min_clip:&lt;minimum clip length&gt;,
128 read_group:&lt;string&gt;
129
130 -pe bam_file:&lt;file name&gt;,
131 id:&lt;sample name&gt;,
132 histo_file:&lt;file name&gt;,
133 mean:&lt;value&gt;,
134 stdev:&lt;value&gt;,
135 read_length:&lt;length&gt;,
136 min_non_overlap:&lt;length&gt;,
137 discordant_z:&lt;z value&gt;,
138 back_distance:&lt;distance&gt;,
139 min_mapping_threshold:&lt;mapping quality&gt;,
140 weight:&lt;sample weight&gt;,
141 read_group:&lt;string&gt;
142
143 -bedpe bedpe_file:&lt;bedpe file&gt;,
144 id:&lt;sample name&gt;,
145 weight:&lt;sample weight&gt;
146
97 </help> 147 </help>
98 148
99 <citations> 149 <citations>
100 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> 150 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
101 </citations> 151 </citations>