Mercurial > repos > iuc > varscan_mpileup

annotate macros.xml @ 3:ee62c46d9cbe draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 79f2f0e89e74348cf18602e83762a0cb26131f17
author iuc
date Tue, 04 Dec 2018 05:51:02 -0500
parents d062703d6f13
children e3f170cc4f95
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
1 <macros>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
2 <xml name="requirements">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
3 <requirements>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
4 <requirement type="package" version="@VERSION@">varscan</requirement>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
5 <yield/>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
6 </requirements>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
7 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
8
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
9 <token name="@VERSION@">2.4.3</token>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
10
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
11 <xml name="stdio">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
12 <stdio>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
13 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
14 <regex match=".*" source="both" level="log" description="tool progress"/>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
15 </stdio>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
16 <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
17 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
18
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
19 <xml name="citations">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
20 <citations>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
21 <citation type="doi">10.1101/gr.129684.111</citation>
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
22 <citation type="doi">10.1002/0471250953.bi1504s44</citation>
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
23 </citations>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
24 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
25
1
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
26 <xml name="input_pileups">
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
27 <conditional name="pileup">
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
28 <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help="">
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
29 <option value="separated">As separated normal and tumor files</option>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
30 <option value="combined">Normal and Tumor combined in one file</option>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
31 </param>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
32 <when value="separated">
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
33 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
34 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
35 </when>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
36 <when value="combined">
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
37 <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
38 </when>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
39 </conditional>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
40 </xml>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
41
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
42 <token name="@INPUT_PILEUPS@">
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
43 #if $pileup.pileup_select == 'separated'
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
44 '${pileup.normal_pileup}'
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
45 '${pileup.tumor_pileup}'
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
46 galaxy_out
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
47 #else:
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
48 '${pileup.combined_pileup}'
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
49 galaxy_out
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
50 --mpileup 1
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
51 #end if
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
52
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
53 </token>
0bc800d67a0e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
54
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
55 <xml name="min_coverage" token_help="Minimum depth at a position to make a call">
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
57 label="Minimum coverage" help="@HELP@"/>
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
58 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
59 <xml name="min_reads2">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
60 <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
61 label="Minimum supporting reads" help="Minimum number of variant-supporting reads at a position required to make a call"/>
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
62 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
63 <xml name="min_avg_qual">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
64 <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
65 label="Minimum base quality"
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
66 help="The minimum base quality at the variant position required to use a read for calling" />
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
67 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
68 <xml name="min_var_freq" token_value="0.01">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
69 <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
70 label="Minimum variant allele frequency"
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
71 help="Minimum variant allele frequency required for calling a variant"/>
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
72 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
73 <xml name="min_freq_for_hom">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
74 <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
75 label="Minimum homozygous variant allele frequency"
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
76 help="Minimum variant allele frequency required for calling a homozygous genotype" />
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
77 </xml>
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
78 <xml name="p_value" token_value="0.01"
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
79 token_label="p-value threshold for calling variants"
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
80 token_help="">
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
81 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1"
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
82 label="@LABEL@" help="@HELP@"/>
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
83 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
84 <xml name="strand_filter">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
85 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
86 <option value="no" selected="True">no</option>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
87 <option value="yes">yes</option>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
88 </param>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
89 </xml>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
90
2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
91 <token name="@HELP_HEADER@"><![CDATA[
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
92 **VarScan Overview**
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
93
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
94 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
95
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
96 .. _VarScan: http://dkoboldt.github.io/varscan/
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
97 .. _here: http://dkoboldt.github.io/varscan/using-varscan.html
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
98 ]]></token>
0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
99 </macros>