Commit a5b33529 authored by Takadonet's avatar Takadonet

fix bug where output from tools was not being redirect into galaxy output file.

parent 278d82fe
<tool id="filterstat" name="Filter Stats" version ="0.0.1">
<tool id="filterstat" name="Filter Stats" version ="0.0.2">
<description>Identify number of positions excluded based on filtered status</description>
<requirements>
<requirement type="package" version="1.3">snvphyl</requirement>
......@@ -6,10 +6,11 @@
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/filter-stats.pl -i $tabfile -o $out
/\$VCF2PSEUDO/filter-stats.pl -i $tabfile
#if $summary == "invalids":
-a
#end if
> $out
</command>
<inputs>
<param name="tabfile" type="data" label="Pseudo-alignment positions tab delimited file" format="tabular"/>
......
<tool id="verify_map" name="Verify Mapping Quality" version="0.0.1">
<tool id="verify_map" name="Verify Mapping Quality" version="0.0.2">
<description>Checks the mapping quality of all BAM files generated in the core SNP pipeline.</description>
<requirements>
<requirement type="package" version="1.3">snvphyl</requirement>
......@@ -11,10 +11,12 @@
#for $f in $bams.keys# --bam "$f=$bams[$f]" #end for#
#if $mindepth :
--min-depth $mindepth
#end if
#if $minmap :
#end if
#if $minmap :
--min-map $minmap
#end ifs
#end if
> $output_log
</command>
<inputs>
......
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