Mercurial > repos > iuc > gemini_burden

comparison gemini_burden.xml @ 5:699ce2631e79 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:52:15 -0500
parents c70d79e0eed7
children f0bf88e9e689
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4:c70d79e0eed7 5:699ce2631e79
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
2 <description>perform sample-wise gene-level burden calculations</description> 2 <description>perform sample-wise gene-level burden calculations</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">burden</token> 5 <token name="@BINARY@">burden</token>
6 <token name="@GEMINI_BUG_WARNING@">Caveat: due to a bug in this version of GEMINI, filtering on alternate allele frequency will get disabled when you select 'All non-synonymous variants' as the types of variants to be used for the burden calculations above.</token> 6 <token name="@GEMINI_BUG_WARNING@">Caveat: due to a bug in this version of GEMINI, filtering on alternate allele frequency will get disabled when you select 'All non-synonymous variants' as the types of variants to be used for the burden calculations above.</token>
23 --min-aaf ${analysis.min_aaf} 23 --min-aaf ${analysis.min_aaf}
24 --max-aaf ${analysis.max_aaf} 24 --max-aaf ${analysis.max_aaf}
25 --permutations ${analysis.permutations} 25 --permutations ${analysis.permutations}
26 ${analysis.save_tscores} 26 ${analysis.save_tscores}
27 #end if 27 #end if
28 "$infile" 28 '$infile'
29 > "$outfile" 29 > '$outfile'
30 #if str($analysis.mode) == "c-alpha" and $analysis.save_tscores: 30 #if str($analysis.mode) == "c-alpha" and $analysis.save_tscores:
31 && touch permutated_t_scores.txt 31 && touch permutated_t_scores.txt
32 && mv permutated_t_scores.txt $t_scores 32 && mv permutated_t_scores.txt $t_scores
33 #end if 33 #end if
34 ]]> 34 ]]>