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comparison snp_caller_caller.xml @ 23:5db0545b9004 draft

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update to v0.1.7.3
author wolma
date Thu, 21 Jul 2016 03:55:49 -0400
parents c46406466625
children
comparison
equal deleted inserted replaced
22:24154c580718 23:5db0545b9004
1 <tool id="variant_calling" name="Variant Calling" version="0.1.7.2"> 1 <tool id="variant_calling" name="Variant Calling" version="0.1.7.3">
2 <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description> 2 <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements" />
7 <version_command>python3 -m MiModD version -q</version_command> 7 <version_command>python3 -m MiModD version -q</version_command>
8 <command> 8 <command>
9 python3 -m MiModD varcall 9 python3 -m MiModD varcall
10 10
11 "$ref_genome" 11 "$ref_genome"
19 --verbose 19 --verbose
20 --quiet 20 --quiet
21 </command> 21 </command>
22 22
23 <inputs> 23 <inputs>
24 <param name="ref_genome" type="data" format="fasta" label="reference genome" /> 24 <param format="fasta" label="reference genome" name="ref_genome" type="data" />
25 <repeat name="list_input" title="Aligned reads input source" default="1" min="1"> 25 <repeat default="1" min="1" name="list_input" title="Aligned reads input source">
26 <param name="inputfile" type="data" format="bam" label="input file" /> 26 <param format="bam" label="input file" name="inputfile" type="data" />
27 </repeat> 27 </repeat>
28 <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="false" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." /> 28 <param checked="false" falsevalue="" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." label="group reads based on read group id only" name="group_by_id" truevalue="-i" type="boolean" />
29 <param name="no_md5_check" type="boolean" label="turn off md5 sum verification" truevalue="-x" falsevalue="" checked="false" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." /> 29 <param checked="false" falsevalue="" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." label="turn off md5 sum verification" name="no_md5_check" truevalue="-x" type="boolean" />
30 <param name="depth" type="integer" value="250" label="maximum per-BAM depth (default: 250)" help="to avoid excessive use of memory"/> 30 <param help="to avoid excessive use of memory" label="maximum per-BAM depth (default: 250)" name="depth" type="integer" value="250" />
31 </inputs> 31 </inputs>
32 32
33 <outputs> 33 <outputs>
34 <data name="output_vcf" format="bcf" label="Variant Calls from MiModd Variant Calling on ${on_string}"/> 34 <data format="bcf" label="Variant Calls from MiModd Variant Calling on ${on_string}" name="output_vcf" />
35 </outputs> 35 </outputs>
36 36
37 <help> 37 <help>
38 .. class:: infomark 38 .. class:: infomark
39 39