Mercurial > repos > dave > lofreq_call

annotate lofreq_call.xml @ 0:b37a6b94e9fe 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/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
author dave
date Wed, 27 Nov 2019 15:25:33 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
1 <tool id="lofreq_call" name="Call variants" version="@WRAPPER_VERSION@0">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
2 <description>with LoFreq</description>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
3 <macros>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
4 <import>macros.xml</import>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
5 </macros>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
6 <expand macro="requirements" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
8 ## prepare reference genome and mapped reads input
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
9 @PREPARE_REF@
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
10 ln -s '$reads' reads.bam &&
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
11 ln -s -f '${reads.metadata.bam_index}' reads.bam.bai &&
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
12
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
13 ## call variants with lofreq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
14
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
15 ## make lofreq stick to tool contract by
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
16 ## generating tmp output inside job working dir
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
17 mkdir pp-tmp &&
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
18 export TMPDIR=pp-tmp &&
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
19
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
20 lofreq call-parallel
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
21
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
22 --ref '$reference_fasta_fn' --out variants.vcf --pp-threads \${GALAXY_SLOTS:-1}
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
23
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
24 #if $advanced_options.option_selector == 'yes'
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
25 #if $advanced_options.regions.bed
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
26 --bed '$advanced_options.regions.bed'
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
27 #end if
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
28 #if $advanced_options.source_qual.ign_vcf
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
29 --ign-vcf '$advanced_options.source_qual.ign_vcf'
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
30 #end if
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
31 #if $advanced_options.regions.region
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
32 --region $advanced_options.regions.region
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
33 #end if
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
34 #if $advanced_options.pval.bonf
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
35 --bonf $advanced_options.pval.bonf
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
36 #else
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
37 --bonf dynamic
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
38 #end if
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
39 --min-bq $advanced_options.bc_quals.min_bq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
40 --min-alt-bq $advanced_options.bc_quals.min_alt_bq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
41 --def-alt-bq $advanced_options.bc_quals.def_alt_bq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
42 --min-jq $advanced_options.bc_quals.min_jq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
43 --min-alt-jq $advanced_options.bc_quals.min_alt_jq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
44 --def-alt-jq $advanced_options.bc_quals.def_alt_jq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
45 --min-mq $advanced_options.map_quals.min_mq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
46 --max-mq $advanced_options.map_quals.max_mq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
47 --def-nm-q $advanced_options.source_qual.def_nm_q
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
48 --sig $advanced_options.pval.sig
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
49 --min-cov $advanced_options.misc.min_cov
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
50 --max-depth $advanced_options.misc.max_depth
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
51 $advanced_options.align_quals.no_baq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
52 $advanced_options.align_quals.no_idaq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
53 $advanced_options.align_quals.del_baq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
54 $advanced_options.align_quals.no_ext_baq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
55 $advanced_options.map_quals.no_mq
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
56 $advanced_options.indels.call_indels
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
57 $advanced_options.indels.only_indels
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
58 $advanced_options.source_qual.src_qual
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
59 $advanced_options.misc.use_orphan
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
60 $advanced_options.misc.plp_summary_only
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
61 $advanced_options.misc.no_default_filter
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
62 #end if
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
63
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
64 reads.bam 2>&1
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
65
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
66 ## in case of errors add the log files produced
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
67 ## by the parallel workers to stderr
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
68 || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
69 ]]></command>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
70 <inputs>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
71 <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
72 <expand macro="reference_interface" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
73 <conditional name="advanced_options">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
74 <param name="option_selector" type="select" label="Advanced options">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
75 <option value="no" selected="true">Use defaults</option>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
76 <option value="yes">Specify parameters</option>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
77 </param>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
78 <when value="no" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
79 <when value="yes">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
80 <section name="regions" title="Regions" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
81 <param argument="--bed" type="data" format="bed" optional="true" label="BED file with regions to examine" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
82 <param argument="--region" type="text" label="Limit calls to this region" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
83 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
84 <section name="bc_quals" title="Base-calling quality" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
85 <param name="min_bq" argument="--min-bq" type="integer" value="6" label="Mimimum baseQ" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
86 <param name="min_alt_bq" argument="--min-alt-bq" type="integer" value="6" label="Mimimum baseQ for alternate bases" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
87 <param name="def_alt_bq" argument="--def-alt-bq" type="integer" value="0" label="Overwrite baseQs of alternate bases with this value" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
88 <param name="min_jq" argument="--min-jq" type="integer" value="0" label="Minimum joinedQ" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
89 <param name="min_alt_jq" argument="--min-alt-jq" type="integer" value="0" label="Minimum joinedQ for alternate bases" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
90 <param name="def_alt_jq" argument="--def-alt-jq" type="integer" value="0" label="Overwrite joinedQs of alternate bases with this value" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
91 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
92 <section name="align_quals" title="Base alignment quality" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
93 <param name="no_baq" argument="--no-baq" type="boolean" truevalue="--no-baq" falsevalue="" label="Disable use of base-alignment quality" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
94 <param name="no_idaq" argument="--no-idaq" type="boolean" truevalue="--no-idaq" falsevalue="" label="Don't use IDAQ values" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
95 <param name="del_baq" argument="--del-baq" type="boolean" truevalue="--del-baq" falsevalue="" label="Delete pre-existing BAQ values" help="Computes BAQ values regardless of their presence in the input BAM" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
96 <param name="no_ext_baq" argument="--no-ext-baq" type="boolean" truevalue="--no-ext-baq" falsevalue="" label="Do not use external BAQ" help="Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
97 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
98 <section name="map_quals" title="Mapping quality" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
99 <param name="min_mq" argument="--min-mq" type="integer" value="0" label="Minimum mapping quality" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
100 <param name="max_mq" argument="--max-mq" type="integer" value="255" label="Maximum mapping quality" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
101 <param name="no_mq" argument="--no-mq" type="boolean" truevalue="--src-qua" falsevalue="" label="Don't merge mapping quality" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
102 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
103 <section name="indels" title="Indels" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
104 <param name="call_indels" argument="--call-indels" type="boolean" truevalue="--call-indels" falsevalue="" label="Enable indel calls" help="Note: This adds a preprocessing step to include indel alignment qualities" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
105 <param name="only_indels" argument="--only-indels" type="boolean" truevalue="--only-indels" falsevalue="" label="Only call indels; no SNVs" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
106 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
107 <section name="source_qual" title="Source quality" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
108 <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf" optional="true" label="Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
109 <param name="src_qual" argument="--src-qual" type="boolean" truevalue="--src-qua" falsevalue="" label="Enable computation of source quality" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
110 <param name="def_nm_q" argument="--def-nm-q" type="integer" value="-1" label="Replace non-match base qualities with this value" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
111 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
112 <section name="pval" title="P-values" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
113 <param argument="--sig" type="float" value="0.01" label="P-Value cutoff" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
114 <param argument="--bonf" type="integer" optional="true" label="Bonferroni factor" help="Leave unset to increase the factor per performed test or specify a factor here" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
115 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
116 <section name="misc" title="Other options" expanded="false">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
117 <param name="min_cov" argument="--min-cov" type="integer" value="1" label="Test only positions having at least this coverage" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
118 <param name="max_depth" argument="--max-depth" type="integer" value="1000000" label="Cap coverage at this depth" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
119 <param name="use_orphan" argument="--use-orphan" type="boolean" truevalue="--use-orphan" falsevalue="" label="Count anomalous read pairs" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
120 <param name="plp_summary_only" argument="--plp-summary-only" type="boolean" truevalue="--plp-summary-only" falsevalue="" label="No variant calling, just output pileup summary per column" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
121 <param name="no_default_filter" argument="--no-default-filter" type="boolean" truevalue="--no-default-filter" falsevalue="" label="Don't run default 'lofreq filter' automatically after calling variants" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
122 </section>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
123 </when>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
124 </conditional>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
125 </inputs>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
126 <outputs>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
127 <data name="variants" from_work_dir="variants.vcf" format="vcf" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
128 </outputs>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
129 <tests>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
130 <test>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
131 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
132 <param name="ref_selector" value="history" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
133 <param name="ref" ftype="fasta" value="pBR322.fa" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
134 <output name="variants" file="call-out1.vcf" lines_diff="4" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
135 </test>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
136 </tests>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
137 <help><![CDATA[
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
138 lofreq call: call variants from BAM file
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
139
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
140 Usage: lofreq call [options] in.bam
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
141
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
142 Options:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
143
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
144 - Reference:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
145 -f | --ref FILE Indexed reference fasta file (gzip supported) [null]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
146
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
147 - Output:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
148 -o | --out FILE Vcf output file [- = stdout]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
149
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
150 - Regions:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
151 -r | --region STR Limit calls to this region (chrom:start-end) [null]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
152 -l | --bed FILE List of positions (chr pos) or regions (BED) [null]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
153
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
154 - Base-call quality:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
155 -q | --min-bq INT Skip any base with baseQ smaller than INT [6]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
156 -Q | --min-alt-bq INT Skip alternate bases with baseQ smaller than INT [6]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
157 -R | --def-alt-bq INT Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
158 -j | --min-jq INT Skip any base with joinedQ smaller than INT [0]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
159 -J | --min-alt-jq INT Skip alternate bases with joinedQ smaller than INT [0]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
160 -K | --def-alt-jq INT Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
161
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
162 - Base-alignment (BAQ) and indel-aligment (IDAQ) qualities:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
163 -B | --no-baq Disable use of base-alignment quality (BAQ)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
164 -A | --no-idaq Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
165 -D | --del-baq Delete pre-existing BAQ values, i.e. compute even if already present in BAM
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
166 -e | --no-ext-baq Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
167
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
168 - Mapping quality:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
169 -m | --min-mq INT Skip reads with mapping quality smaller than INT [0]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
170 -M | --max-mq INT Cap mapping quality at INT [255]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
171 -N | --no-mq Don't merge mapping quality in LoFreq's model
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
172
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
173 - Indels:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
174 --call-indels Enable indel calls (note: preprocess your file to include indel alignment qualities!)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
175 --only-indels Only call indels; no SNVs
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
176
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
177 - Source quality:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
178 -s | --src-qual Enable computation of source quality
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
179 -S | --ign-vcf FILE Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
180 -T | --def-nm-q INT If >= 0, then replace non-match base qualities with this default value [-1]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
181
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
182 - P-values:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
183 -a | --sig P-Value cutoff / significance level [0.010000]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
184 -b | --bonf Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
185
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
186 - Misc.:
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
187 -C | --min-cov INT Test only positions having at least this coverage [1]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
188 (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
189 -d | --max-depth INT Cap coverage at this depth [1000000]
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
190 --illumina-1.3 Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
191 --use-orphan Count anomalous read pairs (i.e. where mate is not aligned properly)
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
192 --plp-summary-only No variant calling. Just output pileup summary per column
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
193 --no-default-filter Don't run default 'lofreq filter' automatically after calling variants
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
194 --force-overwrite Overwrite any existing output
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
195 --verbose Be verbose
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
196 --debug Enable debugging
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
197
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
198 ]]></help>
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
199 <expand macro="citations" />
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
parents:
diff changeset
200 </tool>