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comparison muse_call.xml @ 4:3112ea6b2c52 draft

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author elixir-it
date Thu, 25 Oct 2018 04:45:32 -0400
parents fe9b86b5da79
children 723755ec06be
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3:b3152fc222fb 4:3112ea6b2c52
8 <import>muse_macros.xml</import> 8 <import>muse_macros.xml</import>
9 </macros> 9 </macros>
10 <command> <![CDATA[ 10 <command> <![CDATA[
11 ##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
12 12
13 samtools index $input2 && samtools index $input3 && 13 samtools index $input2 2> log && samtools index $input3 2>log &&
14 14
15 MuSE call -O variant_call 15 MuSE call -O variant_call
16 #if $reference_source.reference_source_selector == "history" 16 #if $reference_source.reference_source_selector == "history"
17 -f $reference_source.reference 17 -f $reference_source.reference
18 #end if 18 #end if
39 <outputs> 39 <outputs>
40 <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/> 40 <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
41 </outputs> 41 </outputs>
42 <tests> 42 <tests>
43 <test> 43 <test>
44 <param name="input1" value="test_fasta.fa" ftype="fasta"/> 44 <param name="input1" value="test_fasta.fa" ftype="fasta"/>
45 <param name="input2" value="Muse_test_tumoral.bam"/> 45 <param name="input2" value="Muse_test_tumoral.bam"/>
46 <param name="input3" value="Muse_test_normal.bam"/> 46 <param name="input3" value="Muse_test_normal.bam"/>
47 <output name="output" file="results.txt" lines_diff="8"/> 47 <output name="output" file="results.txt" lines_diff="8"/>
48 </test> 48 </test>
49 </tests> 49 </tests>