Mercurial > repos > elixir-it > muse

comparison muse_call.xml @ 1:fe9b86b5da79 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Thu, 18 Oct 2018 08:06:06 -0400
parents c4f5e1994690
children 3112ea6b2c52
comparison
equal deleted inserted replaced
0:c4f5e1994690 1:fe9b86b5da79
2 <description>First step of somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data.</description> 2 <description>First step of somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.rc" >muse</requirement> 4 <requirement type="package" version="1.0.rc" >muse</requirement>
5 <requirement type="package" version="1.7">samtools</requirement> 5 <requirement type="package" version="1.7">samtools</requirement>
6 </requirements> 6 </requirements>
7 <macros>
8 <import>muse_macros.xml</import>
9 </macros>
7 <command> <![CDATA[ 10 <command> <![CDATA[
8 ##creation of the bam indexes and execution of the MuSE call command with all the advanced options 11 ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
9 samtools index $input2 && samtools index $input3 && MuSE call -O variant_call -f $input1 $input2 $input3 12
13 samtools index $input2 && samtools index $input3 &&
14
15 MuSE call -O variant_call
16 #if $reference_source.reference_source_selector == "history"
17 -f $reference_source.reference
18 #end if
19 #if $reference_source.reference_source_selector == "cached"
20 -f $reference_source.ref_file.fields.path
21 #end if
22
23 $input2 $input3
24
10 #if $region 25 #if $region
11 -r $region 26 -r $region
12 #end if 27 #end if
13 #if $positions 28 #if $positions
14 -l $positions 29 -l $positions
15 #end if]]> 30 #end if]]>
16 </command> 31 </command>
17 <inputs> 32 <inputs>
18 <param format="fasta" name="input1" type="data" label="reference" help="fasta"/> 33 <expand macro="reference_loc"/>
19 <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/> 34 <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/>
20 <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/> 35 <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/>
21 <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/> 36 <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/>
22 <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" /> 37 <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" />
23 </inputs> 38 </inputs>