Mercurial > repos > iuc > gemini_set_somatic
view gemini_set_somatic.xml @ 6:3208dd1dbfe2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"
author | iuc |
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date | Fri, 24 Jan 2020 17:39:33 -0500 |
parents | 991049484627 |
children | 7814e39409d1 |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@"> <description>Tag somatic mutations in a GEMINI database</description> <macros> <import>gemini_macros.xml</import> <token name="@BINARY@">set_somatic</token> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ cp '$infile' '$outfile' && gemini @BINARY@ #if float($min_depth) >= 0: --min-depth $min_depth #end if #if float($min_quality) >= 0: --min-qual $min_quality #end if #if float($min_somatic_score) >= 0: --min-somatic-score $min_somatic_score #end if #if float($max_norm_alt_freq) >= 0: --max-norm-alt-freq $max_norm_alt_freq #end if #if int($max_norm_alt_count) >= 0: --max-norm-alt-count $max_norm_alt_count #end if #if int($min_norm_depth) >= 0: --min-norm-depth $min_norm_depth #end if #if float($min_tumor_alt_freq) >= 0: --min-tumor-alt-freq $min_tumor_alt_freq #end if #if int($min_tumor_alt_count) >= 0: --min-tumor-alt-count $min_tumor_alt_count #end if #if int($min_tumor_depth) >= 0: --min-tumor-depth $min_tumor_depth #end if #if str($chrom).strip(): --chrom '$chrom' #end if '$outfile' ]]> </command> <inputs> <expand macro="infile" /> <param name="min_depth" type="float" value="-1" label="The min combined depth for tumor + normal" help="default: -1 (not set) (--min-depth)"/> <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min-qual)"/> <param name="min_somatic_score" type="float" value="-1" label="The min somatic score (SSC)" help="default: -1 (not set) (--min-somatic-score)"/> <param name="max_norm_alt_freq" type="float" value="-1" label="The max frequency of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-freq)"/> <param name="max_norm_alt_count" type="integer" value="-1" min="-1" label="The max count of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-count)"/> <param name="min_norm_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the normal sample to believe somatic" help="default: -1 (not set) (--min-norm-depth)"/> <param name="min_tumor_alt_freq" type="float" value="-1" label="The minimum frequency of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-freq)"/> <param name="min_tumor_alt_count" type="integer" value="-1" min="-1" label="The minimum count of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-count)"/> <param name="min_tumor_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the tumor sample to believe somatic" help="default: -1 (not set) (--min-tumor-depth)"/> <param name="chrom" type="text" label="A specific chromosome on which to tag somatic mutations" help="e.g. chrom12 (--chrom)" /> </inputs> <outputs> <data name="outfile" format="gemini.sqlite" /> </outputs> <tests> <test> <!-- A very basic test with a nonsensical input db. The example databases that would produce something meaningful are >100 Mbyte --> <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> <param name="min_somatic_score" value="5.65" /> <output name="outfile" file="gemini_is_somatic_result.db" /> </test> </tests> <help> <![CDATA[ **What it does** Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database. ]]> </help> <expand macro="citations"/> </tool>