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comparison muse_call.xml @ 5:723755ec06be draft

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author elixir-it
date Fri, 20 Sep 2019 08:22:09 -0400
parents 3112ea6b2c52
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4:3112ea6b2c52 5:723755ec06be
1 <tool id="muse_call" name="muse call" version="1.0.rc"> 1 <tool id="muse_call" name="muse call" version="1.0.rc">
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 <requirement type="package" version="1.0" >openssl</requirement>
6 </requirements> 7 </requirements>
7 <macros> 8 <macros>
8 <import>muse_macros.xml</import> 9 <import>muse_macros.xml</import>
9 </macros> 10 </macros>
10 <command> <![CDATA[ 11 <command> <![CDATA[
11 ##creation of the bam indexes and execution of the MuSE call command with all the advanced options 12 ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
12 13
13 samtools index $input2 2> log && samtools index $input3 2>log && 14 samtools index $input2 2> $log && samtools index $input3 2> $log &&
14 15
15 MuSE call -O variant_call 16 MuSE call -O variant_call
16 #if $reference_source.reference_source_selector == "history" 17 #if $reference_source.reference_source_selector == "history"
17 -f $reference_source.reference 18 -f $reference_source.reference
18 #end if 19 #end if
25 #if $region 26 #if $region
26 -r $region 27 -r $region
27 #end if 28 #end if
28 #if $positions 29 #if $positions
29 -l $positions 30 -l $positions
30 #end if]]> 31 #end if
32 2> $log
33 ]]>
31 </command> 34 </command>
32 <inputs> 35 <inputs>
33 <expand macro="reference_loc"/> 36 <expand macro="reference_loc"/>
34 <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/> 37 <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/>
35 <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/> 38 <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/>
36 <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/> 39 <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/>
37 <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" /> 40 <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" />
38 </inputs> 41 </inputs>
39 <outputs> 42 <outputs>
40 <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/> 43 <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
44 <data format="txt" name="log" label="${tool.name} on ${on_string} log"/>
41 </outputs> 45 </outputs>
42 <tests> 46 <tests>
43 <test> 47 <test>
44 <param name="input1" value="test_fasta.fa" ftype="fasta"/> 48 <param name="input1" value="test_fasta.fa" ftype="fasta"/>
45 <param name="input2" value="Muse_test_tumoral.bam"/> 49 <param name="input2" value="Muse_test_tumoral.bam"/>