Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 78:bd5fd2f82f3c draft
Uploaded
author | yhoogstrate |
---|---|
date | Wed, 11 Jun 2014 04:52:55 -0400 |
parents | f89704ed1d8f |
children | 5fd919686c2d |
files | varscan_mpileup2snp.xml varscan_mpileup2snp_from_bam.xml |
diffstat | 2 files changed, 19 insertions(+), 15 deletions(-) [+] |
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--- a/varscan_mpileup2snp.xml Tue Jun 10 10:42:22 2014 -0400 +++ b/varscan_mpileup2snp.xml Wed Jun 11 04:52:55 2014 -0400 @@ -21,8 +21,8 @@ $varscan_variants #end if - #if $varscan_output_vcf - --output-vcf 1 + #if $varscan_output == "vcf" + --output-vcf 1 #end if 2> stderr.txt @@ -52,13 +52,16 @@ </when> </conditional> - <param type="boolean" name="varscan_output_vcf" falsevalue="0" truevalue="1" label="VarScan: If set to 1, outputs in VCF format" /> + <param name="varscan_output" type="select" label="Output format"> + <option value="vcf">VCF</option> + <option value="tabular">tabular</option> + </param> </inputs> <outputs> <data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}"> <change_format> - <when input="varscan_output_vcf" value="1" format="vcf" /> + <when input="varscan_output" value="vcf" format="vcf" /> </change_format> </data> </outputs> @@ -69,7 +72,6 @@ <param name="parameters" value="default" /> <param name="varscan_output_vcf" value="1" /> - <output name="snv_output" file="hg19_mutant.vcf" /> </test> </tests>
--- a/varscan_mpileup2snp_from_bam.xml Tue Jun 10 10:42:22 2014 -0400 +++ b/varscan_mpileup2snp_from_bam.xml Wed Jun 11 04:52:55 2014 -0400 @@ -79,7 +79,7 @@ #end for 2>stderr_1.txt - #if $sort_mpileup + #if $mpileup_parallelization.sort_mpileup | sort -k 1,1 -k 2,2 #end if @@ -99,7 +99,7 @@ $varscan_variants #end if - #if $varscan_output_vcf + #if $varscan_output == "vcf" --output-vcf 1 #end if @@ -132,10 +132,10 @@ <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option> </param> <when value="history"> - <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (fasta)" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> + <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (FASTA)" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> </when> <when value="indexed_filtered"> - <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" > + <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > <options from_data_table="all_fasta"> <column name="name" index="2"/> <column name="dbkey" index="1"/> @@ -146,7 +146,7 @@ </param> </when> <when value="indexed_all"> - <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" > + <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > <options from_data_table="all_fasta"> <column name="name" index="2"/> <column name="dbkey" index="1"/> @@ -167,7 +167,7 @@ </param> <when value="entire_genome" /> <when value="region"> - <param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="chr:pos or chr:start-end" /> + <param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" /> </when> <when value="regions_file_pos"> <param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" /> @@ -185,11 +185,10 @@ <when value="false" /> <when value="true"> <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" /> + <param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file (SLOW)" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> </when> </conditional> - <param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> - <conditional name="extended_parameters"> <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings."> <option value="default">Default settings</option> @@ -229,13 +228,16 @@ </when> </conditional> - <param type="boolean" name="varscan_output_vcf" falsevalue="0" truevalue="1" label="VarScan: If set to 1, outputs in VCF format" /> + <param name="varscan_output" type="select" label="Output format"> + <option value="vcf">VCF</option> + <option value="tabular">tabular</option> + </param> </inputs> <outputs> <data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}"> <change_format> - <when input="varscan_output_vcf" value="1" format="vcf" /> + <when input="varscan_output" value="vcf" format="vcf" /> </change_format> </data> </outputs>